Changes in src/molecule_graph.cpp [e5ad5c:1f1b23]

File:

• src/molecule_graph.cpp (modified) (5 diffs)

src/molecule_graph.cpp

@@ -147 +147 @@
         for (LC->n[2] = 0; LC->n[2] < LC->N[2]; LC->n[2]++) {
           const LinkedNodes *List = LC->GetCurrentCell();
-//          Log() << Verbose(2) << "Current cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << " containing " << List->size() << " points." << endl;
+          //Log() << Verbose(2) << "Current cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << " containing " << List->size() << " points." << endl;
           if (List != NULL) {
             for (LinkedNodes::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
               Walker = AtomMap[(*Runner)->nr];
-//              Log() << Verbose(0) << "Current Atom is " << *Walker << "." << endl;
+              //Log() << Verbose(0) << "Current Atom is " << *Walker << "." << endl;
               // 3c. check for possible bond between each atom in this and every one in the 27 cells
               for (n[0] = -1; n[0] <= 1; n[0]++)
@@ -157 +157 @@
                   for (n[2] = -1; n[2] <= 1; n[2]++) {
                     const LinkedNodes *OtherList = LC->GetRelativeToCurrentCell(n);
-//                    Log() << Verbose(2) << "Current relative cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << " containing " << List->size() << " points." << endl;
+                    //Log() << Verbose(2) << "Current relative cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << " containing " << List->size() << " points." << endl;
                     if (OtherList != NULL) {
                       for (LinkedNodes::const_iterator OtherRunner = OtherList->begin(); OtherRunner != OtherList->end(); OtherRunner++) {
                         if ((*OtherRunner)->nr > Walker->nr) {
                           OtherWalker = AtomMap[(*OtherRunner)->nr];
-//                          Log() << Verbose(0) << "Current other Atom is " << *OtherWalker << "." << endl;
+                          //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 = OtherWalker->x.PeriodicDistanceSquared(&(Walker->x), cell_size);
-//                          Log() << Verbose(1) << "Checking distance " << distance << " against typical bond length of " << bonddistance*bonddistance << "." << endl;
-                          (BG->*minmaxdistance)(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
                           const bool status = (distance <= MaxDistance * MaxDistance) && (distance >= MinDistance * MinDistance);
-//                          Log() << Verbose(1) << "MinDistance is " << MinDistance << " and MaxDistance is " << MaxDistance << "." << endl;
-                          if (OtherWalker->father->nr > Walker->father->nr) {
-                            if (status) { // create bond if distance is smaller
-//                              Log() << Verbose(1) << "Adding Bond between " << *Walker << " and " << *OtherWalker << " in distance " << sqrt(distance) << "." << endl;
-                              AddBond(Walker->father, OtherWalker->father, 1); // also increases molecule::BondCount
-                            } else {
-//                              Log() << Verbose(1) << "Not Adding: distance too great." << endl;
-                            }
+                          if ((OtherWalker->father->nr > Walker->father->nr) && (status)) { // create bond if distance is smaller
+                            //Log() << Verbose(1) << "Adding Bond between " << *Walker << " and " << *OtherWalker << " in distance " << sqrt(distance) << "." << endl;
+                            AddBond(Walker->father, OtherWalker->father, 1); // also increases molecule::BondCount
                           } else {
-//                            Log() << Verbose(1) << "Not Adding: Wrong order of labels." << endl;
+                            //Log() << Verbose(1) << "Not Adding: Wrong label order or distance too great." << endl;
                           }
                         }
@@ -932 +926 @@
         break; // breaking here will not cause error!
     }
-    if (i == vertex->ListOfBonds.size())
+    if (i == vertex->ListOfBonds.size()) {
       eLog() << Verbose(0) << "Error: All Component entries are already occupied!" << endl;
-  } else
+      performCriticalExit();
+    }
+  } else {
     eLog() << Verbose(0) << "Error: Given vertex is NULL!" << endl;
+    performCriticalExit();
+  }
 }
 ;
@@ -994 +992 @@
   Log() << Verbose(1) << "Saving adjacency list ... ";
   if (AdjacencyFile != NULL) {
+    AdjacencyFile << "m\tn" << endl;
     ActOnAllAtoms(&atom::OutputAdjacency, &AdjacencyFile);
     AdjacencyFile.close();
+    Log() << Verbose(1) << "done." << endl;
+  } else {
+    Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl;
+    status = false;
+  }
+
+  return status;
+}
+;
+
+/** Storing the bond structure of a molecule to file.
+ * Simply stores Atom::nr and then the Atom::nr of all bond partners, one per line.
+ * \param *out output stream for debugging
+ * \param *path path to file
+ * \return true - file written successfully, false - writing failed
+ */
+bool molecule::StoreBondsToFile(char *path)
+{
+  ofstream BondFile;
+  stringstream line;
+  bool status = true;
+
+  line << path << "/" << FRAGMENTPREFIX << ADJACENCYFILE;
+  BondFile.open(line.str().c_str(), ios::out);
+  Log() << Verbose(1) << "Saving adjacency list ... ";
+  if (BondFile != NULL) {
+    BondFile << "m\tn" << endl;
+    ActOnAllAtoms(&atom::OutputBonds, &BondFile);
+    BondFile.close();
     Log() << Verbose(1) << "done." << endl;
   } else {
@@ -1119 +1147 @@
   bool status = true;
   if (ReferenceStack->IsEmpty()) {
-    eLog() << Verbose(0) << "ReferenceStack is empty!" << endl;
+    Log() << Verbose(1) << "ReferenceStack is empty!" << endl;
     return false;
   }