Changes in src/molecule_graph.cpp [aafd77:c27778]

File:

• src/molecule_graph.cpp (modified) (8 diffs)

src/molecule_graph.cpp

@@ -5 +5 @@
  *      Author: heber
  */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
 
 #include "Helpers/MemDebug.hpp"
@@ -22 +18 @@
 #include "linkedcell.hpp"
 #include "lists.hpp"
-#include "verbose.hpp"
 #include "log.hpp"
+#include "memoryallocator.hpp"
 #include "molecule.hpp"
 #include "World.hpp"
 #include "Helpers/fast_functions.hpp"
 #include "Helpers/Assert.hpp"
-#include "Matrix.hpp"
-#include "Box.hpp"
-#include "stackclass.hpp"
+
 
 struct BFSAccounting
@@ -127 +121 @@
   LinkedCell *LC = NULL;
   bool free_BG = false;
-  Box &domain = World::getInstance().getDomain();
+  double * const cell_size = World::getInstance().getDomain();
 
   if (BG == NULL) {
@@ -184 +178 @@
                           //Log() << Verbose(1) << "Checking distance " << OtherWalker->x.PeriodicDistanceSquared(&(Walker->x), cell_size) << " against typical bond length of " << bonddistance*bonddistance << "." << endl;
                           (BG->*minmaxdistance)(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
-                          const double distance = domain.periodicDistanceSquared(OtherWalker->x,Walker->x);
+                          const double distance = OtherWalker->x.PeriodicDistanceSquared(Walker->x,cell_size);
                           const bool status = (distance <= MaxDistance * MaxDistance) && (distance >= MinDistance * MinDistance);
 //                          Log() << Verbose(1) << "MinDistance is " << MinDistance << " and MaxDistance is " << MaxDistance << "." << endl;
@@ -585 +579 @@
     // From OldGraphNr to CurrentGraphNr ranges an disconnected subgraph
     DoLog(0) && (Log() << Verbose(0) << "Disconnected subgraph ranges from " << OldGraphNr << " to " << DFS.CurrentGraphNr << "." << endl);
-    LeafWalker->Leaf->Output((ofstream *)&(Log() << Verbose(0)));
+    LeafWalker->Leaf->Output((ofstream *)&cout);
     DoLog(0) && (Log() << Verbose(0) << endl);
 
@@ -670 +664 @@
   BFS.ColorList = new enum Shading[AtomCount];
   BFS.BFSStack = new StackClass<atom *> (AtomCount);
+  BFS.TouchedStack = new StackClass<atom *> (AtomCount);
 
   for (int i = AtomCount; i--;) {
     BFS.ShortestPathList[i] = -1;
     BFS.PredecessorList[i] = 0;
+    BFS.ColorList[i] = white;
   }
 };
@@ -687 +683 @@
   delete[](BFS.ColorList);
   delete (BFS.BFSStack);
+  delete (BFS.TouchedStack);
   BFS.AtomCount = 0;
 };
@@ -831 +828 @@
       MinRingSize = RingSize;
   } else {
-    DoLog(1) && (Log() << Verbose(1) << "No ring containing " << *BFS.Root << " with length equal to or smaller than " << MinimumRingSize[Walker->GetTrueFather()->nr] << " found." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "No ring containing " << *BFS.Root << " with length equal to or smaller than " << MinimumRingSize[BFS.Root->GetTrueFather()->nr] << " found." << endl);
   }
 };