Changes in src/atom.cpp [1b2d30:ad2b411]

File:

• src/atom.cpp (modified) (11 diffs)

src/atom.cpp

@@ -4 +4 @@
  *
  */
+
+#include "Helpers/MemDebug.hpp"
 
 #include "atom.hpp"
@@ -14 +16 @@
 #include "vector.hpp"
 #include "World.hpp"
+#include "molecule.hpp"
 
 /************************************* Functions for class atom *************************************/
@@ -21 +24 @@
  */
 atom::atom() :
-  previous(NULL), next(NULL), father(this), sort(&nr)
+  father(this), sort(&nr), mol(0)
 {
   node = &x;  // TesselPoint::x can only be referenced from here
@@ -29 +32 @@
  */
 atom::atom(atom *pointer) :
-    ParticleInfo(pointer),
-    previous(NULL), next(NULL), father(pointer), sort(&nr)
+    ParticleInfo(pointer),father(pointer), sort(&nr)
 {
   type = pointer->type;  // copy element of atom
@@ -37 +39 @@
   FixedIon = pointer->FixedIon;
   node = &x;
+  mol = 0;
 };
 
 atom *atom::clone(){
   atom *res = new atom(this);
-  res->previous=0;
-  res->next=0;
   res->father = this;
   res->sort = &res->nr;
@@ -50 +51 @@
   res->FixedIon = FixedIon;
   res->node = &x;
+  res->mol = 0;
   World::getInstance().registerAtom(res);
   return res;
@@ -59 +61 @@
 atom::~atom()
 {
+  removeFromMolecule();
+  for(BondList::iterator iter=ListOfBonds.begin(); iter!=ListOfBonds.end();){
+    // deleting the bond will invalidate the iterator !!!
+    bond *bond =*(iter++);
+    delete(bond);
+  }
 };
 
@@ -67 +75 @@
 atom *atom::GetTrueFather()
 {
-  atom *walker = this;
-  do {
-    if (walker == walker->father) // top most father is the one that points on itself
-      break;
-    walker = walker->father;
-  } while (walker != NULL);
-  return walker;
+  if(father == this){ // top most father is the one that points on itself
+    return this;
+  }
+  else if(!father) {
+    return 0;
+  }
+  else {
+    return father->GetTrueFather();
+  }
 };
 
@@ -149 +159 @@
   * \return true - \a *out present, false - \a *out is NULL
  */
-bool atom::OutputArrayIndexed(ostream * const out, const int *ElementNo, int *AtomNo, const char *comment) const
+bool atom::OutputArrayIndexed(ofstream * const out, const int *ElementNo, int *AtomNo, const char *comment) const
 {
   AtomNo[type->Z]++;  // increment number
@@ -226 +236 @@
  * \param *AtomNo pointer to atom counter that is increased by one
  */
-void atom::OutputMPQCLine(ostream * const out, const Vector *center, int *AtomNo = NULL) const
+void atom::OutputMPQCLine(ofstream * const out, const Vector *center, int *AtomNo = NULL) const
 {
   *out << "\t\t" << type->symbol << " [ " << x[0]-center->at(0) << "\t" << x[1]-center->at(1) << "\t" << x[2]-center->at(2) << " ]" << endl;
@@ -305 +315 @@
 }
 
-atomId_t atom::getId() {
+atomId_t atom::getId() const {
   return id;
 }
+
+void atom::setMolecule(molecule *_mol){
+  // take this atom from the old molecule
+  removeFromMolecule();
+  mol = _mol;
+  if(!mol->containsAtom(this)){
+    mol->AddAtom(this);
+  }
+}
+
+void atom::removeFromMolecule(){
+  if(mol){
+    if(mol->containsAtom(this)){
+      mol->erase(this);
+    }
+    mol=0;
+  }
+}
+
 
 atom* NewAtom(atomId_t _id){