Calling Model::clear() in the middle of an UndoState would cause a cr…

…ash when replaying the state, since Atoms were not renumbered during the clear.

src/model/atom.cpp

@@ -253,12 +253,7 @@ Atom** Model::atomArray()
 void Model::clearAtoms()
 {
 	Messenger::enter("Model::clearAtoms");
-	Atom* i = atoms_.first();
-	while (i != NULL)
-	{
-		deleteAtom(i, true);
-		i = atoms_.first();
-	}
+	while (Atom *i = atoms_.last()) deleteAtom(i, true);
 	Messenger::exit("Model::clearAtoms");
 }
 
@@ -622,4 +617,4 @@ void Model::swapAtoms(Atom* i, Atom* j)
 void Model::swapAtoms(int id1, int id2)
 {
 	swapAtoms(atom(id1), atom(id2));
-}
+}

src/model/cell.cpp

@@ -506,6 +506,7 @@ void Model::replicateCell(const Vec3<double>& negativeCells, const Vec3<double>&
 	}
 
 	logChange(Log::Structure);
+
 	Messenger::exit("Model::replicateCell");
 }
 

src/undo/atom_creation.cpp

@@ -56,6 +56,7 @@ void AtomCreationEvent::undo(Model* m)
 	Messenger::enter("AtomCreationEvent::undo");
 	Atom** modelatoms = m->atomArray();
 	int id;
+
 	// Atom creation (UndoEvent::Redo) and deletion (UndoEvent::Undo)
 	if (direction_ == UndoEvent::Undo)
 	{

src/undo/undostate.cpp

@@ -118,5 +118,5 @@ bool UndoState::doLogsDiffer() const
 // Print changes in state
 void UndoState::print() const
 {
-	for (UndoEvent* u = events_.first(); u != NULL; u = u->prev) u->print();
+	for (UndoEvent* u = events_.first(); u != NULL; u = u->next) u->print();
 }