Changes in src/moleculelist.cpp [244a84:58ed4a]

File:

• src/moleculelist.cpp (modified) (12 diffs)

src/moleculelist.cpp

@@ -19 +19 @@
 #include "memoryallocator.hpp"
 #include "periodentafel.hpp"
+#include "World.hpp"
 
 /*********************************** Functions for class MoleculeListClass *************************/
@@ -313 +314 @@
   Tesselation *TesselStruct = NULL;
   if ((srcmol == NULL) || (mol == NULL)) {
-    eLog() << Verbose(1) << "Either fixed or variable molecule is given as NULL." << endl;
+    DoeLog(1) && (eLog()<< Verbose(1) << "Either fixed or variable molecule is given as NULL." << endl);
     return false;
   }
@@ -321 +322 @@
   FindNonConvexBorder(mol, TesselStruct, (const LinkedCell *&)LCList, 4., NULL);
   if (TesselStruct == NULL) {
-    eLog() << Verbose(1) << "Could not tesselate the fixed molecule." << endl;
+    DoeLog(1) && (eLog()<< Verbose(1) << "Could not tesselate the fixed molecule." << endl);
     return false;
   }
@@ -442 +443 @@
     input.open(line.c_str());
     if (input == NULL) {
-      eLog() << Verbose(0) << endl << "Unable to open " << line << ", is the directory correct?" << endl;
+      DoeLog(0) && (eLog()<< Verbose(0) << endl << "Unable to open " << line << ", is the directory correct?" << endl);
       performCriticalExit();
       return false;
@@ -638 +639 @@
   int FragmentCounter = 0;
   ofstream output;
-
+  double cell_size_backup[6];
+  double * const cell_size = World::get()->cell_size;
+
+  // backup cell_size
+  for (int i=0;i<6;i++)
+    cell_size_backup[i] = cell_size[i];
   // store the fragments as config and as xyz
   for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
@@ -646 +652 @@
       strcpy(PathBackup, path);
     else {
-      eLog() << Verbose(0) << "OutputConfigForListOfFragments: NULL default path obtained from config!" << endl;
+      DoeLog(0) && (eLog()<< Verbose(0) << "OutputConfigForListOfFragments: NULL default path obtained from config!" << endl);
       performCriticalExit();
     }
@@ -682 +688 @@
       j += k + 1;
       BoxDimension.x[k] = 2.5 * (configuration->GetIsAngstroem() ? 1. : 1. / AtomicLengthToAngstroem);
-      (*ListRunner)->cell_size[j] += BoxDimension.x[k] * 2.;
+      cell_size[j] = BoxDimension.x[k] * 2.;
     }
     (*ListRunner)->Translate(&BoxDimension);
@@ -724 +730 @@
   // printing final number
   Log() << Verbose(2) << "Final number of fragments: " << FragmentCounter << "." << endl;
+
+  // restore cell_size
+  for (int i=0;i<6;i++)
+    cell_size[i] = cell_size_backup[i];
 
   return result;
@@ -776 +786 @@
 
   // 1. dissect the molecule into connected subgraphs
-  configuration->BG->ConstructBondGraph(mol);
+  if (!configuration->BG->ConstructBondGraph(mol)) {
+    delete (mol);
+    DoeLog(1) && (eLog()<< Verbose(1) << "There are no bonds." << endl);
+    return;
+  }
 
   // 2. scan for connected subgraphs
@@ -783 +797 @@
   Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
   delete(BackEdgeStack);
+  if ((Subgraphs == NULL) || (Subgraphs->next == NULL)) {
+    delete (mol);
+    DoeLog(1) && (eLog()<< Verbose(1) << "There are no atoms." << endl);
+    return;
+  }
 
   // 3. dissect (the following construct is needed to have the atoms not in the order of the DFS, but in
@@ -824 +843 @@
     Walker = mol->start->next;
     if ((Walker->nr <0) || (Walker->nr >= mol->AtomCount)) {
-      eLog() << Verbose(0) << "Index of atom " << *Walker << " is invalid!" << endl;
+      DoeLog(0) && (eLog()<< Verbose(0) << "Index of atom " << *Walker << " is invalid!" << endl);
       performCriticalExit();
     }
@@ -833 +852 @@
       molecules[FragmentCounter-1]->AddAtom(Walker);    // counting starts at 1
     } else {
-      eLog() << Verbose(0) << "Atom " << *Walker << " not associated to molecule!" << endl;
+      DoeLog(0) && (eLog()<< Verbose(0) << "Atom " << *Walker << " not associated to molecule!" << endl);
       performCriticalExit();
     }