Changes in src/moleculelist.cpp [ca2587:437922]

File:

• src/moleculelist.cpp (modified) (7 diffs)

src/moleculelist.cpp

@@ -35 +35 @@
  * \return true - add successful
  */
-bool MoleculeListClass::insert(molecule *mol)
+void MoleculeListClass::insert(molecule *mol)
 {
   mol->IndexNr = MaxIndex++;
@@ -128 +128 @@
   atom *Walker = NULL;
   int Counts[MAX_ELEMENTS];
+  double size=0;
+  Vector Origin;
 
   // header
-  *out << "Index\tName\tNo.Atoms\tformula" << endl;
+  *out << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
   cout << Verbose(0) << "-----------------------------------------------" << endl;
   if (ListOfMolecules.size() == 0)
     *out << "\tNone" << endl;
   else {
+    Origin.Zero();
     for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
       // reset element counts
       for (int j = 0; j<MAX_ELEMENTS;j++)
         Counts[j] = 0;
-      // count atoms per element
+      // count atoms per element and determine size of bounding sphere
+      size=0.;
       Walker = (*ListRunner)->start;
       while (Walker->next != (*ListRunner)->end) {
         Walker = Walker->next;
         Counts[Walker->type->Z]++;
+        if (Walker->x.DistanceSquared(&Origin) > size)
+          size = Walker->x.DistanceSquared(&Origin);
       }
       // output Index, Name, number of atoms, chemical formula
       *out << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t";
       Elemental = (*ListRunner)->elemente->end;
-      while(Elemental != (*ListRunner)->elemente->start) {
+      while(Elemental->previous != (*ListRunner)->elemente->start) {
         Elemental = Elemental->previous;
         if (Counts[Elemental->Z] != 0)
           *out << Elemental->symbol << Counts[Elemental->Z];
       }
-      *out << endl;
+      // Center and size
+      *out << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
     }
   }
@@ -164 +171 @@
 molecule * MoleculeListClass::ReturnIndex(int index)
 {
-  int count = 1;
-  MoleculeList::iterator ListRunner = ListOfMolecules.begin();
-  for(; ((ListRunner != ListOfMolecules.end()) && (count < index)); ListRunner++);
-  if (count == index)
-    return (*ListRunner);
-  else
-    return NULL;
+  for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
+    if ((*ListRunner)->IndexNr == index)
+      return (*ListRunner);
+  return NULL;
 };
 
@@ -523 +527 @@
 
   // open file for the force factors
-  *out << Verbose(1) << "Saving force factors ... ";
+  *out << Verbose(1) << "Saving  force factors ... ";
   line << path << "/" << FRAGMENTPREFIX << FORCESFILE;
   ForcesFile.open(line.str().c_str(), ios::out);
@@ -691 +695 @@
 MoleculeLeafClass::MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf = NULL)
 {
-  //    if (Up != NULL)
-  //            if (Up->DownLeaf == NULL) // are we the first down leaf for the upper leaf?
-  //                    Up->DownLeaf = this;
-  //    UpLeaf = Up;
-  //    DownLeaf = NULL;
+  //  if (Up != NULL)
+  //    if (Up->DownLeaf == NULL) // are we the first down leaf for the upper leaf?
+  //      Up->DownLeaf = this;
+  //  UpLeaf = Up;
+  //  DownLeaf = NULL;
   Leaf = NULL;
   previous = PreviousLeaf;
@@ -711 +715 @@
 MoleculeLeafClass::~MoleculeLeafClass()
 {
-  //    if (DownLeaf != NULL) {// drop leaves further down
-  //            MoleculeLeafClass *Walker = DownLeaf;
-  //            MoleculeLeafClass *Next;
-  //            do {
-  //                    Next = Walker->NextLeaf;
-  //                    delete(Walker);
-  //                    Walker = Next;
-  //            } while (Walker != NULL);
-  //            // Last Walker sets DownLeaf automatically to NULL
-  //    }
+  //  if (DownLeaf != NULL) {// drop leaves further down
+  //    MoleculeLeafClass *Walker = DownLeaf;
+  //    MoleculeLeafClass *Next;
+  //    do {
+  //      Next = Walker->NextLeaf;
+  //      delete(Walker);
+  //      Walker = Next;
+  //    } while (Walker != NULL);
+  //    // Last Walker sets DownLeaf automatically to NULL
+  //  }
   // remove the leaf itself
   if (Leaf != NULL) {
@@ -729 +733 @@
   if (previous != NULL)
     previous->next = next;
-  //    } else { // we are first in list (connects to UpLeaf->DownLeaf)
-  //            if ((NextLeaf != NULL) && (NextLeaf->UpLeaf == NULL))
-  //                    NextLeaf->UpLeaf = UpLeaf;      // either null as we are top level or the upleaf of the first node
-  //            if (UpLeaf != NULL)
-  //                    UpLeaf->DownLeaf = NextLeaf;    // either null as we are only leaf or NextLeaf if we are just the first
-  //    }
-  //    UpLeaf = NULL;
+  //  } else { // we are first in list (connects to UpLeaf->DownLeaf)
+  //    if ((NextLeaf != NULL) && (NextLeaf->UpLeaf == NULL))
+  //      NextLeaf->UpLeaf = UpLeaf;  // either null as we are top level or the upleaf of the first node
+  //    if (UpLeaf != NULL)
+  //      UpLeaf->DownLeaf = NextLeaf;  // either null as we are only leaf or NextLeaf if we are just the first
+  //  }
+  //  UpLeaf = NULL;
   if (next != NULL) // are we last in list
     next->previous = previous;