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

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 "molecules.hpp"
+#include "element.hpp"
+#include "helpers.hpp"
+#include "linkedcell.hpp"
+#include "molecule.hpp"
 #include "memoryallocator.hpp"
+#include "periodentafel.hpp"
 
 /*********************************** Functions for class MoleculeListClass *************************/
@@ -292 +299 @@
 /** Embedding merge of a given set of molecules into one.
  * Embedding merge inserts one molecule into the other.
- * \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
+ * \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)
 {
-  if (srcmol == NULL)
+  if ((srcmol == NULL) || (mol == NULL)) {
+    cout << Verbose(1) << "ERROR: Either fixed or variable molecule is given as NULL." << endl;
     return false;
-
-  // calculate center for merge
-  srcmol->Center.CopyVector(mol->FindEmbeddingHole((ofstream *)&cout, srcmol));
-  srcmol->Center.Zero();
-
-  // perform simple merge
-  SimpleMerge(mol, srcmol);
+  }
+
+  // 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);
   return true;
 };