Changes in src/molecule_fragmentation.cpp [a67d19:bab12a]

File:

• src/molecule_fragmentation.cpp (modified) (10 diffs)

src/molecule_fragmentation.cpp

@@ -8 +8 @@
 #include <cstring>
 
+#include "World.hpp"
 #include "atom.hpp"
 #include "bond.hpp"
@@ -676 +677 @@
   //if (FragmentationToDo) {    // we should always store the fragments again as coordination might have changed slightly without changing bond structure
   // allocate memory for the pointer array and transmorph graphs into full molecular fragments
-  BondFragments = new MoleculeListClass();
+  BondFragments = new MoleculeListClass(World::getPointer());
   int k=0;
   for(Graph::iterator runner = TotalGraph.begin(); runner != TotalGraph.end(); runner++) {
@@ -721 +722 @@
     // free memory for bond part
     DoLog(1) && (Log() << Verbose(1) << "Freeing bond memory" << endl);
-    delete(FragmentList); // remove bond molecule from memory
+    Free(&FragmentList); // remove bond molecule from memory
     Free(&SortIndex);
   } else {
@@ -906 +907 @@
       }
     } else {
-      DoeLog(1) && (eLog()<< Verbose(1) << "Son " << Runner->Name << " has father " << FatherOfRunner->Name << " but its entry in SonList is " << SonList[FatherOfRunner->nr] << "!" << endl);
+      DoeLog(1) && (eLog()<< Verbose(1) << "Son " << Runner->getName() << " has father " << FatherOfRunner->getName() << " but its entry in SonList is " << SonList[FatherOfRunner->nr] << "!" << endl);
     }
     if ((LonelyFlag) && (Leaf->AtomCount > 1)) {
@@ -929 +930 @@
 {
   atom **SonList = Calloc<atom*>(AtomCount, "molecule::StoreFragmentFromStack: **SonList");
-  molecule *Leaf = new molecule(elemente);
+  molecule *Leaf = World::getInstance().createMolecule();
 
 //  Log() << Verbose(1) << "Begin of StoreFragmentFromKeyset." << endl;
@@ -1657 +1658 @@
   atom *Walker = NULL;
   atom *OtherWalker = NULL;
-  double * const cell_size = World::get()->cell_size;
+  double * const cell_size = World::getInstance().getDomain();
   double *matrix = ReturnFullMatrixforSymmetric(cell_size);
   enum Shading *ColorList = NULL;
@@ -1672 +1673 @@
     // remove bonds that are beyond bonddistance
     for(int i=NDIM;i--;)
-      Translationvector.x[i] = 0.;
+      Translationvector[i] = 0.;
     // scan all bonds
     Binder = first;
@@ -1679 +1680 @@
       Binder = Binder->next;
       for (int i=NDIM;i--;) {
-        tmp = fabs(Binder->leftatom->x.x[i] - Binder->rightatom->x.x[i]);
+        tmp = fabs(Binder->leftatom->x[i] - Binder->rightatom->x[i]);
         //Log() << Verbose(3) << "Checking " << i << "th distance of " << *Binder->leftatom << " to " << *Binder->rightatom << ": " << tmp << "." << endl;
         if (tmp > BondDistance) {
@@ -1693 +1694 @@
       // create translation vector from their periodically modified distance
       for (int i=NDIM;i--;) {
-        tmp = Binder->leftatom->x.x[i] - Binder->rightatom->x.x[i];
+        tmp = Binder->leftatom->x[i] - Binder->rightatom->x[i];
         if (fabs(tmp) > BondDistance)
-          Translationvector.x[i] = (tmp < 0) ? +1. : -1.;
+          Translationvector[i] = (tmp < 0) ? +1. : -1.;
       }
       Translationvector.MatrixMultiplication(matrix);
       //Log() << Verbose(3) << "Translation vector is ";
-      Translationvector.Output();
-      DoLog(0) && (Log() << Verbose(0) << endl);
+      Log() << Verbose(0) << Translationvector <<  endl;
       // apply to all atoms of first component via BFS
       for (int i=AtomCount;i--;)
@@ -1709 +1709 @@
         //Log() << Verbose (3) << "Current Walker is: " << *Walker << "." << endl;
         ColorList[Walker->nr] = black;    // mark as explored
-        Walker->x.AddVector(&Translationvector); // translate
+        Walker->x += Translationvector; // translate
         for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
           if ((*Runner) != Binder) {