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

File:

• src/atom.cpp (modified) (11 diffs)

src/atom.cpp

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