Changes in src/Atom/atom_bondedparticle.cpp [8cc22f:5aaa43]

File:

• src/Atom/atom_bondedparticle.cpp (modified) (7 diffs)

src/Atom/atom_bondedparticle.cpp

@@ -52 +52 @@
 BondedParticle::BondedParticle()
 {
-  ListOfBonds.insert( std::make_pair(0, emptyList) );
+  ListOfBonds.push_back(BondList());
 };
 
@@ -59 +59 @@
 BondedParticle::~BondedParticle()
 {
-  for(BondTrajectory_t::iterator iter = ListOfBonds.begin(); !ListOfBonds.empty();
-      iter = ListOfBonds.begin()) {
-    removeAllBonds(iter->first);
-    ListOfBonds.erase(iter);
-  }
+  removeAllBonds();
 };
 
@@ -224 +220 @@
 }
 
-/** Removes all bonds in current timestep and their instances, too.
+/** Removes all bonds in all timesteps and their instances, too.
  *
  */
 void BondedParticle::removeAllBonds()
 {
-  removeAllBonds(WorldTime::getTime());
+  for (size_t index = 0; index < ListOfBonds.size(); ++index)
+    removeAllBonds(index);
 }
 
@@ -239 +236 @@
 {
   //LOG(3,"INFO: Clearing all bonds of " << *this << ": " << ListOfBonds[_step]);
-  BondTrajectory_t::iterator listiter = ListOfBonds.find(_step);
-  if (listiter != ListOfBonds.end())
-    for (BondList::iterator iter = listiter->second.begin();
-        !listiter->second.empty();
-        iter = listiter->second.begin()) {
-      //LOG(3,"INFO: Clearing bond (" << *iter << ") " << *(*iter) << " of list " << &ListOfBonds);
-      atom * const Other = (*iter)->GetOtherAtom(this);
-      ASSERT( Other != NULL,
-          "BondedParticle::removeAllBonds() - cannot find bond partner for "
-          +toString(**iter)+".");
-      Other->UnregisterBond(_step, *iter);
-      UnregisterBond(_step, *iter);
-    }
+  for (BondList::iterator iter = (ListOfBonds[_step]).begin();
+      !(ListOfBonds[_step]).empty();
+      iter = (ListOfBonds[_step]).begin()) {
+    //LOG(3,"INFO: Clearing bond (" << *iter << ") " << *(*iter) << " of list " << &ListOfBonds);
+    atom * const Other = (*iter)->GetOtherAtom(this);
+    ASSERT( Other != NULL,
+        "BondedParticle::removeAllBonds() - cannot find bond partner for "
+        +toString(**iter)+".");
+    Other->UnregisterBond(_step, *iter);
+    UnregisterBond(_step, *iter);
+  }
 }
 
@@ -265 +260 @@
     if (Binder->Contains(this)) {
       //LOG(3,"INFO: Registering bond "<< *Binder << " with atom " << *this << " at step " << _step);
-      std::pair< BondTrajectory_t::iterator, bool> inserter =
-          ListOfBonds.insert( std::make_pair( _step, BondList(1, Binder)) );
-      if (!inserter.second)
-        inserter.first->second.push_back(Binder);
+      if (ListOfBonds.size() <= _step)
+        ListOfBonds.resize(_step+1);
+      ListOfBonds[_step].push_back(Binder);
       if (WorldTime::getTime() == _step)
         NOTIFY(AtomObservable::BondsAdded);
@@ -296 +290 @@
       OBSERVE;
       //LOG(0,"INFO: Unregistering bond "<< *Binder << " from list " << &ListOfBonds << " of atom " << *this << " at step " << step);
-      BondTrajectory_t::iterator listiter = ListOfBonds.find(_step);
-      if (listiter != ListOfBonds.end()) {
 #ifndef NDEBUG
-        BondList::const_iterator iter =
-            std::find(listiter->second.begin(), listiter->second.end(), Binder);
-        ASSERT( iter != listiter->second.end(),
-            "BondedParticle::UnregisterBond() - "+toString(*Binder)+" not contained at "
-            +toString(_step));
+      BondList::const_iterator iter =
+          std::find(ListOfBonds[_step].begin(), ListOfBonds[_step].end(), Binder);
+      ASSERT( iter != ListOfBonds[_step].end(),
+          "BondedParticle::UnregisterBond() - "+toString(*Binder)+" not contained at "
+          +toString(_step));
 #endif
-        Binder->removeAtom(this);
-        listiter->second.remove(Binder);
-        if (WorldTime::getTime() == _step)
-          NOTIFY(AtomObservable::BondsRemoved);
-        status = true;
-      }
+      Binder->removeAtom(this);
+      ListOfBonds[_step].remove(Binder);
+      if (WorldTime::getTime() == _step)
+        NOTIFY(AtomObservable::BondsRemoved);
+      status = true;
     } else {
       ELOG(1, *Binder << " does not contain " << *this << ".");
@@ -337 +328 @@
 {
   int step = -1;
-  for(BondTrajectory_t::const_iterator listiter = ListOfBonds.begin();
-      listiter != ListOfBonds.end();
-      ++listiter) {
-    for (BondList::const_iterator bonditer = listiter->second.begin();
-        bonditer != listiter->second.end();
+  int tempstep = 0;
+  for(std::vector<BondList>::const_iterator iter = ListOfBonds.begin();
+      iter != ListOfBonds.end();
+      ++iter,++tempstep) {
+    for (BondList::const_iterator bonditer = iter->begin();
+        bonditer != iter->end();
         ++bonditer) {
       if ((*bonditer) == Binder) {
-        step = listiter->first;
+        step = tempstep;
         break;
       }