Changes in src/moleculelist.cpp [f66195:29812d]

File:

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

src/moleculelist.cpp

@@ -5 +5 @@
  */
 
-#include "atom.hpp"
-#include "bond.hpp"
-#include "boundary.hpp"
 #include "config.hpp"
-#include "element.hpp"
-#include "helpers.hpp"
-#include "linkedcell.hpp"
-#include "molecule.hpp"
+#include "molecules.hpp"
 #include "memoryallocator.hpp"
-#include "periodentafel.hpp"
 
 /*********************************** Functions for class MoleculeListClass *************************/
@@ -299 +292 @@
 /** 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!
+ * \param *mol destination molecule
+ * \param *srcmol source molecule
+ * \return true - merge successful, false - merge failed (probably due to non-existant indices
+ * \TODO find embedding center
  */
 bool MoleculeListClass::EmbedMerge(molecule *mol, molecule *srcmol)
 {
-  if ((srcmol == NULL) || (mol == NULL)) {
-    cout << Verbose(1) << "ERROR: Either fixed or variable molecule is given as NULL." << endl;
+  if (srcmol == NULL)
     return false;
-  }
-
-  // calculate envelope for *mol
-  LinkedCell *LCList = new LinkedCell(mol, 8.);
-  FindNonConvexBorder((ofstream *)&cout, mol, LCList, 4., NULL);
-  if (mol->TesselStruct == NULL) {
-    cout << Verbose(1) << "ERROR: Could not tesselate the fixed molecule." << endl;
-    return false;
-  }
-  delete(LCList);
-  LCList = new LinkedCell(mol->TesselStruct, 8.);  // re-create with boundary points only!
-
-  // prepare index list for bonds
-  srcmol->CountAtoms((ofstream *)&cout);
-  atom ** CopyAtoms = new atom*[srcmol->AtomCount];
-  for(int i=0;i<srcmol->AtomCount;i++)
-    CopyAtoms[i] = NULL;
-
-  // for each of the source atoms check whether we are in- or outside and add copy atom
-  atom *Walker = srcmol->start;
-  int nr=0;
-  while (Walker->next != srcmol->end) {
-    Walker = Walker->next;
-    cout << Verbose(2) << "INFO: Current Walker is " << *Walker << "." << endl;
-    if (!mol->TesselStruct->IsInnerPoint((ofstream *)&cout, Walker->x, LCList)) {
-      CopyAtoms[Walker->nr] = new atom(Walker);
-      mol->AddAtom(CopyAtoms[Walker->nr]);
-      nr++;
-    } else {
-      // do nothing
-    }
-  }
-  cout << Verbose(1) << nr << " of " << srcmol->AtomCount << " atoms have been merged.";
-
-  // go through all bonds and add as well
-  bond *Binder = srcmol->first;
-  while(Binder->next != srcmol->last) {
-    Binder = Binder->next;
-    cout << Verbose(3) << "Adding Bond between " << *CopyAtoms[Binder->leftatom->nr] << " and " << *CopyAtoms[Binder->rightatom->nr]<< "." << endl;
-    mol->AddBond(CopyAtoms[Binder->leftatom->nr], CopyAtoms[Binder->rightatom->nr], Binder->BondDegree);
-  }
-  delete(LCList);
+
+  // calculate center for merge
+  srcmol->Center.CopyVector(mol->FindEmbeddingHole((ofstream *)&cout, srcmol));
+  srcmol->Center.Zero();
+
+  // perform simple merge
+  SimpleMerge(mol, srcmol);
   return true;
 };