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

File:

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

src/moleculelist.cpp

@@ -193 +193 @@
       }
       // Center and size
-      Vector *Center = (*ListRunner)->DetermineCenterOfAll();
-      (*out) << "\t" << *Center << "\t" << sqrt(size) << endl;
-      delete(Center);
+      (*out) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
     }
   }
@@ -212 +210 @@
 };
 
+/** 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.