Changes in src/moleculelist.cpp [ad011c:4c2643]

File:

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

src/moleculelist.cpp ¶

@@ -506 +506 @@
   RealSpaceMatrix cell_size = World::getInstance().getDomain().getM();
   RealSpaceMatrix cell_size_backup = cell_size;
+  int count=0;
 
   // store the fragments as config and as xyz
@@ -519 +520 @@
 
     // correct periodic
-    (*ListRunner)->ScanForPeriodicCorrection();
+    if ((*ListRunner)->ScanForPeriodicCorrection()) {
+      count++;
+    }
 
     // output xyz file
@@ -543 +546 @@
     // center on edge
     (*ListRunner)->CenterEdge(&BoxDimension);
+    for (int k = 0; k < NDIM; k++)  // if one edge is to small, set at least to 1 angstroem
+      if (BoxDimension[k] < 1.)
+        BoxDimension[k] += 1.;
     (*ListRunner)->SetBoxDimension(&BoxDimension); // update Box of atoms by boundary
     for (int k = 0; k < NDIM; k++) {
@@ -591 +597 @@
   // printing final number
   DoLog(2) && (Log() << Verbose(2) << "Final number of fragments: " << FragmentCounter << "." << endl);
+
+  // printing final number
+  DoLog(0) && (Log() << Verbose(0) << "For " << count << " fragments periodic correction would have been necessary." << endl);
 
   // restore cell_size
@@ -741 +750 @@
   // remove the leaf itself
   if (Leaf != NULL) {
+    Leaf->removeAtomsinMolecule();
     World::getInstance().destroyMolecule(Leaf);
     Leaf = NULL;