Changes in src/config.cpp [112b09:274d45]

File:

• src/config.cpp (modified) (3 diffs)

src/config.cpp

@@ -1784 +1784 @@
   char filename[MAXSTRINGSIZE];
   ofstream output;
-  molecule *mol = World::getInstance().createMolecule();
-  mol->SetNameFromFilename(ConfigFileName);
+  molecule *mol = NULL;
 
   if (!strcmp(configpath, GetDefaultPath())) {
@@ -1816 +1815 @@
   // translate each to its center and merge all molecules in MoleculeListClass into this molecule
   int N = molecules->ListOfMolecules.size();
-  int *src = new int[N];
-  N=0;
-  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
-    src[N++] = (*ListRunner)->IndexNr;
-    (*ListRunner)->Translate(&(*ListRunner)->Center);
-  }
-  molecules->SimpleMultiAdd(mol, src, N);
-  delete[](src);
-
-  // ... and translate back
-  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
-    (*ListRunner)->Center.Scale(-1.);
-    (*ListRunner)->Translate(&(*ListRunner)->Center);
-    (*ListRunner)->Center.Scale(-1.);
+  if (N != 1) { // don't do anything in case of only one molecule (shifts mol ids otherwise)
+    int *src = new int[N];
+    N=0;
+    for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
+      src[N++] = (*ListRunner)->IndexNr;
+      (*ListRunner)->Translate(&(*ListRunner)->Center);
+    }
+    mol = World::getInstance().createMolecule();
+    mol->SetNameFromFilename(ConfigFileName);
+    molecules->SimpleMultiMerge(mol, src, N);
+    mol->doCountAtoms();
+    mol->CountElements();
+    mol->CalculateOrbitals(*this);
+    delete[](src);
+  } else {
+    if (!molecules->ListOfMolecules.empty()) {
+      mol = *(molecules->ListOfMolecules.begin());
+      mol->doCountAtoms();
+      mol->CalculateOrbitals(*this);
+    } else {
+      DoeLog(1) && (eLog() << Verbose(1) << "There are no molecules to save!" << endl);
+    }
   }
 
   Log() << Verbose(0) << "Storing configuration ... " << endl;
   // get correct valence orbitals
-  mol->CalculateOrbitals(*this);
-  InitMaxMinStopStep = MaxMinStopStep = MaxPsiDouble;
   if (ConfigFileName != NULL) { // test the file name
     strcpy(filename, ConfigFileName);
@@ -1895 +1900 @@
   }
 
-  World::getInstance().destroyMolecule(mol);
+  // don't destroy molecule as it contains all our atoms
+  //World::getInstance().destroyMolecule(mol);
 };