Changes in / [95e6b1:7aa3cf]

Location:

src

Files:

• Legacy/oldmenu.cpp (added)
• Legacy/oldmenu.hpp (added)
• UIElements/Views/QT4/QTStatusBar.cpp (modified) (1 diff)
• UIElements/Views/QT4/QTWorldView.cpp (modified) (2 diffs)
• UIElements/Views/QT4/QTWorldView.hpp (modified) (1 diff)
• boundary.cpp (modified) (1 diff)
• config.cpp (modified) (1 diff)
• molecule.hpp (modified) (2 diffs)
• molecule_geometry.cpp (modified) (7 diffs)
• moleculelist.cpp (modified) (2 diffs)
• periodentafel.cpp (modified) (1 diff)

src/UIElements/Views/QT4/QTStatusBar.cpp

@@ -21 +21 @@
   QStatusBar(_parent),
   Observer("QTStatusBar"),
+  parent(_parent),
   atomCount(World::getInstance().numAtoms()),
-  moleculeCount(World::getInstance().numMolecules()),
-  parent(_parent)
+  moleculeCount(World::getInstance().numMolecules())
 {
   World::getInstance().signOn(this);

src/UIElements/Views/QT4/QTWorldView.cpp

@@ -20 +20 @@
 // these attributes are skiped so far
 const int QTWorldView::COLUMNCOUNT = COLUMNTYPES_MAX;
-const char *QTWorldView::COLUMNNAMES[QTWorldView::COLUMNCOUNT]={"Name","Atoms"/*,"Formula"*//*,"Size"*/};
+const char *QTWorldView::COLUMNNAMES[QTWorldView::COLUMNCOUNT]={"Name","Atoms"/*,"Formula"*/,"Center"/*,"Size"*/};
 
 QTWorldView::QTWorldView(QWidget * _parent) :
@@ -81 +81 @@
     setItem(i,ATOMS,countWidget);
 
+    const Vector center = (*iter)->Center;
+    QTableWidgetItem *centerWidget = new QTableWidgetItem();
+    stringstream centersstr;
+    centersstr << center;
+    centerWidget->setText(QString(centersstr.str().c_str()));
+    setItem(i,CENTER,centerWidget);
+    centerWidget->setFlags(Qt::ItemIsSelectable | Qt::ItemIsUserCheckable | Qt::ItemIsEnabled);
+
     molSelection[i]=nameWidget->isSelected();
   }

src/UIElements/Views/QT4/QTWorldView.hpp

@@ -28 +28 @@
 
   static const int COLUMNCOUNT;
-  enum {NAME,ATOMS,COLUMNTYPES_MAX} COLUMNTYPES;
+  enum {NAME,ATOMS,CENTER,COLUMNTYPES_MAX} COLUMNTYPES;
   static const char *COLUMNNAMES[];
 

src/boundary.cpp

@@ -804 +804 @@
   // Center filler at origin
   filler->CenterEdge(&Inserter);
+  filler->Center.Zero();
   const int FillerCount = filler->getAtomCount();
   DoLog(2) && (Log() << Verbose(2) << "INFO: Filler molecule has the following bonds:" << endl);

src/config.cpp

@@ -1586 +1586 @@
     for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
       src[N++] = (*ListRunner)->IndexNr;
+      (*ListRunner)->Translate(&(*ListRunner)->Center);
     }
     mol = World::getInstance().createMolecule();
     mol->SetNameFromFilename(ConfigFileName);
+    molecules->SimpleMultiMerge(mol, src, N);
     //mol->CalculateOrbitals(*this);
     delete[](src);

src/molecule.hpp

@@ -104 +104 @@
     double BondDistance;  //!< typical bond distance used in CreateAdjacencyList() and furtheron
     bool ActiveFlag;    //!< in a MoleculeListClass used to discern active from inactive molecules
-    //Vector Center;      //!< Center of molecule in a global box
+    Vector Center;      //!< Center of molecule in a global box
     int IndexNr;        //!< index of molecule in a MoleculeListClass
     char name[MAXSTRINGSIZE];         //!< arbitrary name
@@ -379 +379 @@
   void eraseMolecule();
 
+
+  // merging of molecules
+  bool SimpleMerge(molecule *mol, molecule *srcmol);
+  bool SimpleAdd(molecule *mol, molecule *srcmol);
+  bool SimpleMultiMerge(molecule *mol, int *src, int N);
+  bool SimpleMultiAdd(molecule *mol, int *src, int N);
+  bool ScatterMerge(molecule *mol, int *src, int N);
+  bool EmbedMerge(molecule *mol, molecule *srcmol);
+
   private:
   World *world; //!< The world this List belongs to. Needed to avoid deadlocks in the destructor

src/molecule_geometry.cpp

@@ -104 +104 @@
     (*max) += (*min);
     Translate(min);
+    Center.Zero();
   }
   delete(min);
@@ -117 +118 @@
   int Num = 0;
   molecule::const_iterator iter = begin();  // start at first in list
-  Vector Center;
 
   Center.Zero();
+
   if (iter != end()) {   //list not empty?
     for (; iter != end(); ++iter) {  // continue with second if present
@@ -127 +128 @@
     Center.Scale(-1./(double)Num); // divide through total number (and sign for direction)
     Translate(&Center);
+    Center.Zero();
   }
 };
@@ -195 +197 @@
 void molecule::CenterPeriodic()
 {
-  Vector NewCenter;
-  DeterminePeriodicCenter(NewCenter);
-  // go through all atoms
-  BOOST_FOREACH(atom* iter, atoms){
-    *iter -= NewCenter;
-  }
+  DeterminePeriodicCenter(Center);
 };
 
@@ -210 +207 @@
 void molecule::CenterAtVector(Vector *newcenter)
 {
-  // go through all atoms
-  BOOST_FOREACH(atom* iter, atoms){
-    *iter -= *newcenter;
-  }
+  Center = *newcenter;
 };
 
@@ -283 +277 @@
   bool flag;
   Vector Testvector, Translationvector;
-  Vector Center;
 
   do {
@@ -329 +322 @@
 
   Center.Scale(1./static_cast<double>(getAtomCount()));
-  CenterAtVector(&Center);
 };
 

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.

src/periodentafel.cpp

@@ -295 +295 @@
     getline(input,header1tmp);
     getline(input,header2tmp); // skip first two header lines
-    //cout << "First header: " << header1tmp << endl;
-    //cout << "Second header: " << header2tmp << endl;
+    cout << "First header: " << header1tmp << endl;
+    cout << "Second header: " << header2tmp << endl;
     DoLog(0) && (Log() << Verbose(0) <<  "Parsed elements:");
     while (!input.eof()) {