Changes in src/moleculelist.cpp [ead4e6:24a5e0]

File:

• src/moleculelist.cpp (modified) (14 diffs)

src/moleculelist.cpp

@@ -141 +141 @@
 void MoleculeListClass::Enumerate(ostream *out)
 {
+  element* Elemental = NULL;
   atom *Walker = NULL;
-  periodentafel *periode = World::getInstance().getPeriode();
-  std::map<atomicNumber_t,unsigned int> counts;
+  int Counts[MAX_ELEMENTS];
   double size=0;
   Vector Origin;
@@ -155 +155 @@
     Origin.Zero();
     for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
+      // reset element counts
+      for (int j = 0; j<MAX_ELEMENTS;j++)
+        Counts[j] = 0;
       // count atoms per element and determine size of bounding sphere
       size=0.;
@@ -160 +163 @@
       while (Walker->next != (*ListRunner)->end) {
         Walker = Walker->next;
-        counts[Walker->type->getNumber()]++;
+        Counts[Walker->type->Z]++;
         if (Walker->x.DistanceSquared(&Origin) > size)
           size = Walker->x.DistanceSquared(&Origin);
@@ -166 +169 @@
       // output Index, Name, number of atoms, chemical formula
       (*out) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t";
-
-      std::map<atomicNumber_t,unsigned int>::reverse_iterator iter;
-      for(iter=counts.rbegin(); iter!=counts.rend();++iter){
-        atomicNumber_t Z =(*iter).first;
-        (*out) << periode->FindElement(Z)->getSymbol() << (*iter).second;
+      Elemental = (*ListRunner)->elemente->end;
+      while(Elemental->previous != (*ListRunner)->elemente->start) {
+        Elemental = Elemental->previous;
+        if (Counts[Elemental->Z] != 0)
+          (*out) << Elemental->symbol << Counts[Elemental->Z];
       }
       // Center and size
@@ -212 +215 @@
   // remove src
   ListOfMolecules.remove(srcmol);
-  World::getInstance().destroyMolecule(srcmol);
+  World::get()->destroyMolecule(srcmol);
   return true;
 };
@@ -577 +580 @@
   stringstream line;
   atom *Walker = NULL;
-  periodentafel *periode=World::getInstance().getPeriode();
+  element *runner = NULL;
 
   // open file for the force factors
@@ -587 +590 @@
     //output << prefix << "Forces" << endl;
     for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
-      periodentafel::const_iterator elemIter;
-      for(elemIter=periode->begin();elemIter!=periode->end();++elemIter){
-          if ((*ListRunner)->ElementsInMolecule[(*elemIter).first]) { // if this element got atoms
+      runner = (*ListRunner)->elemente->start;
+      while (runner->next != (*ListRunner)->elemente->end) { // go through every element
+        runner = runner->next;
+        if ((*ListRunner)->ElementsInMolecule[runner->Z]) { // if this element got atoms
           Walker = (*ListRunner)->start;
           while (Walker->next != (*ListRunner)->end) { // go through every atom of this element
             Walker = Walker->next;
-            if (Walker->type->getNumber() == (*elemIter).first) {
+            if (Walker->type->Z == runner->Z) {
               if ((Walker->GetTrueFather() != NULL) && (Walker->GetTrueFather() != Walker)) {// if there is a rea
                 //Log() << Verbose(0) << "Walker is " << *Walker << " with true father " << *( Walker->GetTrueFather()) << ", it
@@ -746 +750 @@
 void MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration)
 {
-  molecule *mol = World::getInstance().createMolecule();
+  molecule *mol = World::get()->createMolecule();
   atom *Walker = NULL;
   atom *Advancer = NULL;
@@ -771 +775 @@
     }
     // remove the molecule
-    World::getInstance().destroyMolecule(*MolRunner);
+    World::get()->destroyMolecule(*MolRunner);
     ListOfMolecules.erase(MolRunner);
   }
@@ -793 +797 @@
   molecule **molecules = Malloc<molecule *>(MolCount, "config::Load() - **molecules");
   for (int i=0;i<MolCount;i++) {
-    molecules[i] = World::getInstance().createMolecule();
+    molecules[i] = World::get()->createMolecule();
     molecules[i]->ActiveFlag = true;
     strncpy(molecules[i]->name, mol->name, MAXSTRINGSIZE);
@@ -891 +895 @@
   OBSERVE;
   molecule *mol = NULL;
-  mol = World::getInstance().createMolecule();
+  mol = World::get()->createMolecule();
   insert(mol);
 };
@@ -900 +904 @@
   char filename[MAXSTRINGSIZE];
   Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
-  mol = World::getInstance().createMolecule();
+  mol = World::get()->createMolecule();
   do {
     Log() << Verbose(0) << "Enter file name: ";
@@ -958 +962 @@
       mol = *ListRunner;
       ListOfMolecules.erase(ListRunner);
-      World::getInstance().destroyMolecule(mol);
+      World::get()->destroyMolecule(mol);
       break;
     }
@@ -1005 +1009 @@
   // remove the leaf itself
   if (Leaf != NULL) {
-    World::getInstance().destroyMolecule(Leaf);
+    World::get()->destroyMolecule(Leaf);
     Leaf = NULL;
   }