Changes in src/molecule.cpp [274d45:43dad6]

File:

• src/molecule.cpp (modified) (9 diffs)

src/molecule.cpp

@@ -4 +4 @@
  *
  */
-
-#include "Helpers/MemDebug.hpp"
 
 #include <cstring>
@@ -37 +35 @@
  * Initialises molecule list with correctly referenced start and end, and sets molecule::last_atom to zero.
  */
-molecule::molecule(const periodentafel * const teil) :
-  Observable("molecule"),
-  elemente(teil),  MDSteps(0),  BondCount(0), ElementCount(0), NoNonHydrogen(0), NoNonBonds(0),
-  NoCyclicBonds(0), BondDistance(0.),  ActiveFlag(false), IndexNr(-1),
-  formula(this,boost::bind(&molecule::calcFormula,this),"formula"),
-  AtomCount(this,boost::bind(&molecule::doCountAtoms,this),"AtomCount"), last_atom(0),  InternalPointer(atoms.begin())
+molecule::molecule(const periodentafel * const teil) : elemente(teil),
+  MDSteps(0),
+  BondCount(0), ElementCount(0), NoNonHydrogen(0), NoNonBonds(0), NoCyclicBonds(0), BondDistance(0.), 
+  ActiveFlag(false), IndexNr(-1),
+  formula(this,boost::bind(&molecule::calcFormula,this)),
+  AtomCount(this,boost::bind(&molecule::doCountAtoms,this)), last_atom(0),  InternalPointer(begin())
 {
 
@@ -145 +143 @@
   molecule::const_iterator iter = loc;
   iter--;
-  atom* atom = *loc;
-  atomIds.erase( atom->getId() );
-  atoms.remove( atom );
-  atom->removeFromMolecule();
+  atoms.erase( loc );
   return iter;
 }
 
-molecule::const_iterator molecule::erase( atom * key )
+molecule::const_iterator molecule::erase( atom *& key )
 {
   cout << "trying to erase atom" << endl;
   molecule::const_iterator iter = find(key);
   if (iter != end()){
-    atomIds.erase( key->getId() );
-    atoms.remove( key );
-    key->removeFromMolecule();
+    // remove this position and step forward (post-increment)
+    atoms.erase( iter++ );
   }
   return iter;
 }
 
-molecule::const_iterator molecule::find ( atom * key ) const
-{
-  molecule::const_iterator iter;
-  for (molecule::const_iterator Runner = begin(); Runner != end(); ++Runner) {
-    if (*Runner == key)
-      return molecule::const_iterator(Runner);
-  }
-  return molecule::const_iterator(atoms.end());
+molecule::const_iterator molecule::find ( atom *& key ) const
+{
+  return atoms.find( key );
 }
 
 pair<molecule::iterator,bool> molecule::insert ( atom * const key )
 {
-  pair<atomIdSet::iterator,bool> res = atomIds.insert(key->getId());
-  if (res.second) { // push atom if went well
-    atoms.push_back(key);
-    return pair<iterator,bool>(molecule::iterator(--end()),res.second);
-  } else {
-    return pair<iterator,bool>(molecule::iterator(end()),res.second);
-  }
-}
-
-bool molecule::containsAtom(atom* key){
-  return (find(key) != end());
+  pair<atomSet::iterator,bool> res = atoms.insert(key);
+  return pair<iterator,bool>(iterator(res.first,this),res.second);
 }
 
@@ -212 +192 @@
     }
     insert(pointer);
-    pointer->setMolecule(this);
   }
   return true;
@@ -678 +657 @@
 bond * molecule::AddBond(atom *atom1, atom *atom2, int degree)
 {
-  OBSERVE;
   bond *Binder = NULL;
 
@@ -802 +780 @@
   for (molecule::iterator iter = begin(); !empty(); iter = begin())
       erase(iter);
-  return empty();
 };
 
@@ -881 +858 @@
         ElementNo[i] = current++;
     }
-    ActOnAllAtoms( &atom::OutputArrayIndexed, output, (const int *)ElementNo, (int *)AtomNo, (const char *) NULL );
+    ActOnAllAtoms( &atom::OutputArrayIndexed, (ostream * const) output, (const int *)ElementNo, (int *)AtomNo, (const char *) NULL );
     return true;
   }
@@ -1023 +1000 @@
   configuration.MaxPsiDouble /= 2;
   configuration.PsiType = (configuration.PsiMaxNoDown == configuration.PsiMaxNoUp) ? 0 : 1;
-  if ((configuration.PsiType == 1) && (configuration.ProcPEPsi < 2) && ((configuration.PsiMaxNoDown != 1) || (configuration.PsiMaxNoUp != 0))) {
+  if ((configuration.PsiType == 1) && (configuration.ProcPEPsi < 2)) {
     configuration.ProcPEGamma /= 2;
     configuration.ProcPEPsi *= 2;
@@ -1030 +1007 @@
     configuration.ProcPEPsi = 1;
   }
-  cout << configuration.PsiMaxNoDown << ">" << configuration.PsiMaxNoUp << endl;
-  if (configuration.PsiMaxNoDown > configuration.PsiMaxNoUp) {
-    configuration.InitMaxMinStopStep = configuration.MaxMinStopStep = configuration.PsiMaxNoDown;
-    cout << configuration.PsiMaxNoDown << " " << configuration.InitMaxMinStopStep << endl;
-  } else {
-    configuration.InitMaxMinStopStep = configuration.MaxMinStopStep = configuration.PsiMaxNoUp;
-    cout << configuration.PsiMaxNoUp << " " << configuration.InitMaxMinStopStep << endl;
-  }
+  configuration.InitMaxMinStopStep = configuration.MaxMinStopStep = configuration.MaxPsiDouble;
 };