Changes in src/moleculelist.cpp [97b825:61951b]

File:

• src/moleculelist.cpp (modified) (2 diffs)

src/moleculelist.cpp

@@ -193 +193 @@
       }
       // Center and size
-      (*out) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
+      Vector *Center = (*ListRunner)->DetermineCenterOfAll();
+      (*out) << "\t" << *Center << "\t" << sqrt(size) << endl;
+      delete(Center);
     }
   }
@@ -210 +212 @@
 };
 
-/** Simple merge of two molecules into one.
- * \param *mol destination molecule
- * \param *srcmol source molecule
- * \return true - merge successful, false - merge failed (probably due to non-existant indices
- */
-bool MoleculeListClass::SimpleMerge(molecule *mol, molecule *srcmol)
-{
-  if (srcmol == NULL)
-    return false;
-
-  // put all molecules of src into mol
-  for (molecule::iterator iter = srcmol->begin(); !srcmol->empty(); iter=srcmol->begin()) {
-    atom * const Walker = *iter;
-    srcmol->UnlinkAtom(Walker);
-    mol->AddAtom(Walker);
-  }
-
-  // remove src
-  ListOfMolecules.remove(srcmol);
-  World::getInstance().destroyMolecule(srcmol);
-  return true;
-};
-
-/** Simple add of one molecules into another.
- * \param *mol destination molecule
- * \param *srcmol source molecule
- * \return true - merge successful, false - merge failed (probably due to non-existant indices
- */
-bool MoleculeListClass::SimpleAdd(molecule *mol, molecule *srcmol)
-{
-  if (srcmol == NULL)
-    return false;
-
-  // put all molecules of src into mol
-  atom *Walker = NULL;
-  for (molecule::iterator iter = srcmol->begin(); iter != srcmol->end(); ++iter) {
-    Walker = mol->AddCopyAtom((*iter));
-    Walker->father = Walker;
-  }
-
-  return true;
-};
-
-/** Simple merge of a given set of molecules into one.
- * \param *mol destination molecule
- * \param *src index of set of source molecule
- * \param N number of source molecules
- * \return true - merge successful, false - some merges failed (probably due to non-existant indices)
- */
-bool MoleculeListClass::SimpleMultiMerge(molecule *mol, int *src, int N)
-{
-  bool status = true;
-  // check presence of all source molecules
-  for (int i=0;i<N;i++) {
-    molecule *srcmol = ReturnIndex(src[i]);
-    status = status && SimpleMerge(mol, srcmol);
-  }
-  insert(mol);
-  return status;
-};
-
-/** Simple add of a given set of molecules into one.
- * \param *mol destination molecule
- * \param *src index of set of source molecule
- * \param N number of source molecules
- * \return true - merge successful, false - some merges failed (probably due to non-existant indices)
- */
-bool MoleculeListClass::SimpleMultiAdd(molecule *mol, int *src, int N)
-{
-  bool status = true;
-  // check presence of all source molecules
-  for (int i=0;i<N;i++) {
-    molecule *srcmol = ReturnIndex(src[i]);
-    status = status && SimpleAdd(mol, srcmol);
-  }
-  return status;
-};
-
-/** Scatter merge of a given set of molecules into one.
- * Scatter merge distributes the molecules in such a manner that they don't overlap.
- * \param *mol destination molecule
- * \param *src index of set of source molecule
- * \param N number of source molecules
- * \return true - merge successful, false - merge failed (probably due to non-existant indices
- * \TODO find scatter center for each src molecule
- */
-bool MoleculeListClass::ScatterMerge(molecule *mol, int *src, int N)
-{
-  // check presence of all source molecules
-  for (int i=0;i<N;i++) {
-    // get pointer to src molecule
-    molecule *srcmol = ReturnIndex(src[i]);
-    if (srcmol == NULL)
-      return false;
-  }
-  // adapt each Center
-  for (int i=0;i<N;i++) {
-    // get pointer to src molecule
-    molecule *srcmol = ReturnIndex(src[i]);
-    //srcmol->Center.Zero();
-    srcmol->Translate(&srcmol->Center);
-  }
-  // perform a simple multi merge
-  SimpleMultiMerge(mol, src, N);
-  return true;
-};
-
-/** Embedding merge of a given set of molecules into one.
- * Embedding merge inserts one molecule into the other.
- * \param *mol destination molecule (fixed one)
- * \param *srcmol source molecule (variable one, where atoms are taken from)
- * \return true - merge successful, false - merge failed (probably due to non-existant indices)
- * \TODO linked cell dimensions for boundary points has to be as big as inner diameter!
- */
-bool MoleculeListClass::EmbedMerge(molecule *mol, molecule *srcmol)
-{
-  LinkedCell *LCList = NULL;
-  Tesselation *TesselStruct = NULL;
-  if ((srcmol == NULL) || (mol == NULL)) {
-    DoeLog(1) && (eLog()<< Verbose(1) << "Either fixed or variable molecule is given as NULL." << endl);
-    return false;
-  }
-
-  // calculate envelope for *mol
-  LCList = new LinkedCell(mol, 8.);
-  FindNonConvexBorder(mol, TesselStruct, (const LinkedCell *&)LCList, 4., NULL);
-  if (TesselStruct == NULL) {
-    DoeLog(1) && (eLog()<< Verbose(1) << "Could not tesselate the fixed molecule." << endl);
-    return false;
-  }
-  delete(LCList);
-  LCList = new LinkedCell(TesselStruct, 8.);  // re-create with boundary points only!
-
-  // prepare index list for bonds
-  atom ** CopyAtoms = new atom*[srcmol->getAtomCount()];
-  for(int i=0;i<srcmol->getAtomCount();i++)
-    CopyAtoms[i] = NULL;
-
-  // for each of the source atoms check whether we are in- or outside and add copy atom
-  int nr=0;
-  for (molecule::const_iterator iter = srcmol->begin(); iter != srcmol->end(); ++iter) {
-    DoLog(2) && (Log() << Verbose(2) << "INFO: Current Walker is " << **iter << "." << endl);
-    if (!TesselStruct->IsInnerPoint((*iter)->getPosition(), LCList)) {
-      CopyAtoms[(*iter)->nr] = (*iter)->clone();
-      mol->AddAtom(CopyAtoms[(*iter)->nr]);
-      nr++;
-    } else {
-      // do nothing
-    }
-  }
-  DoLog(1) && (Log() << Verbose(1) << nr << " of " << srcmol->getAtomCount() << " atoms have been merged.");
-
-  // go through all bonds and add as well
-  for(molecule::iterator AtomRunner = srcmol->begin(); AtomRunner != srcmol->end(); ++AtomRunner)
-    for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
-      if ((*BondRunner)->leftatom == *AtomRunner) {
-        DoLog(3) && (Log() << Verbose(3) << "Adding Bond between " << *CopyAtoms[(*BondRunner)->leftatom->nr] << " and " << *CopyAtoms[(*BondRunner)->rightatom->nr]<< "." << endl);
-        mol->AddBond(CopyAtoms[(*BondRunner)->leftatom->nr], CopyAtoms[(*BondRunner)->rightatom->nr], (*BondRunner)->BondDegree);
-      }
-  delete(LCList);
-  return true;
-};
 
 /** Simple output of the pointers in ListOfMolecules.