Changes in src/Parser/PcpParser.cpp [14c57a:bd2390]

File:

• src/Parser/PcpParser.cpp (modified) (6 diffs)

src/Parser/PcpParser.cpp

@@ +1 @@
+/*
+ * Project: MoleCuilder
+ * Description: creates and alters molecular systems
+ * Copyright (C)  2010 University of Bonn. All rights reserved.
+ * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
+ */
+
 /*
  * PcpParser.cpp
@@ -348 +355 @@
   // 3. parse the molecule in
   molecule *mol = World::getInstance().createMolecule();
-  MoleculeListClass *molecules = World::getInstance().getMolecules();
-  molecules->insert(mol);
+  mol->ActiveFlag = true;
+  // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
+  World::getInstance().getMolecules()->insert(mol);
   LoadMolecule(mol, FileBuffer, World::getInstance().getPeriode(), FastParsing);
-  //mol->SetNameFromFilename(filename);
-  mol->ActiveFlag = true;
-  //MolList->insert(mol);
 
   // 4. dissect the molecule into connected subgraphs
@@ -478 +483 @@
   PlaneWaveSpecifics.MaxPsiDouble = PlaneWaveSpecifics.PsiMaxNoDown = PlaneWaveSpecifics.PsiMaxNoUp = PlaneWaveSpecifics.PsiType = 0;
   for (vector<atom *>::iterator runner = allatoms.begin(); runner != allatoms.end(); ++runner) {
-    PlaneWaveSpecifics.MaxPsiDouble += (*runner)->getType()->NoValenceOrbitals;
+    PlaneWaveSpecifics.MaxPsiDouble += (*runner)->getType()->getNoValenceOrbitals();
   }
   cout << PlaneWaveSpecifics.MaxPsiDouble << endl;
@@ -513 +518 @@
   // insert all found elements into the map
   for (vector<atom *>::iterator AtomRunner = allatoms.begin();AtomRunner != allatoms.end();++AtomRunner) {
-    Inserter = PresentElements.insert(pair<int, int>((*AtomRunner)->getType()->Z, 1));
+    Inserter = PresentElements.insert(pair<int, int>((*AtomRunner)->getType()->getAtomicNumber(), 1));
     if (!Inserter.second) // increase if present
       Inserter.first->second += 1;
@@ -528 +533 @@
     const element * const elemental = World::getInstance().getPeriode()->FindElement(iter->first);
     ZtoIndexMap.insert( pair<int,int> (iter->first, counter) );
-    *file << "Ion_Type" << counter++ << "\t" << iter->second << "\t" << elemental->Z << "\t1.0\t3\t3\t" << fixed << setprecision(11) << showpoint << elemental->mass << "\t" << elemental->getName() << "\t" << elemental->getSymbol() <<endl;
+    *file << "Ion_Type" << counter++ << "\t" << iter->second << "\t" << elemental->getAtomicNumber() << "\t1.0\t3\t3\t" << fixed << setprecision(11) << showpoint << elemental->getMass() << "\t" << elemental->getName() << "\t" << elemental->getSymbol() <<endl;
   }
 }
@@ -544 +549 @@
   int nr = 0;
   for (vector<atom *>::iterator AtomRunner = allatoms.begin();AtomRunner != allatoms.end();++AtomRunner) {
-    Inserter = ZtoCountMap.insert( pair<int, int>((*AtomRunner)->getType()->Z, 1) );
+    Inserter = ZtoCountMap.insert( pair<int, int>((*AtomRunner)->getType()->getAtomicNumber(), 1) );
     if (!Inserter.second)
       Inserter.first->second += 1;
-    const int Z = (*AtomRunner)->getType()->Z;
+    const int Z = (*AtomRunner)->getType()->getAtomicNumber();
     *file << "Ion_Type" << ZtoIndexMap[Z] << "_" << ZtoCountMap[Z] << "\t"  << fixed << setprecision(9) << showpoint;
     *file << (*AtomRunner)->at(0) << "\t" << (*AtomRunner)->at(1) << "\t" << (*AtomRunner)->at(2);