Changes in / [9a8a6b:6a922b]

Location:

src

Files:

• Graph/BondGraph.hpp (modified) (2 diffs)
• UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) (4 diffs)
• UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) (4 diffs)
• World.cpp (modified) (1 diff)
• molecule.cpp (modified) (11 diffs)
• molecule.hpp (modified) (3 diffs)

src/Graph/BondGraph.hpp

@@ -221 +221 @@
               neighboriter != ListOfNeighbors.end();
               ++neighboriter) {
-            if ((*neighboriter) > Walker) {  // just to not add bonds from both sides
-              const atom * const OtherWalker = dynamic_cast<const atom *>(*neighboriter);
-              ASSERT(OtherWalker != NULL,
-                  "BondGraph::CreateAdjacency() - TesselPoint "
-                  +(*neighboriter)->getName()+" that was not an atom retrieved from LinkedList");
+            const atom * const OtherWalker = dynamic_cast<const atom *>(*neighboriter);
+            ASSERT(OtherWalker != NULL,
+                "BondGraph::CreateAdjacency() - TesselPoint "
+                +(*neighboriter)->getName()+" that was not an atom retrieved from LinkedList");
+            if (OtherWalker->getId() > Walker->getId()) {  // just to not add bonds from both sides
               LOG(4, "INFO: Current other atom is " << *OtherWalker << ".");
 
@@ -245 +245 @@
               }
             } else {
-              LOG(5, "REJECT: Not Adding: Wrong order.");
+              LOG(4, "REJECT: Not Adding: Wrong order.");
             }
           }

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp

@@ -85 +85 @@
 const Observable::channels_t GLMoleculeObject_molecule::AtomsChannels(getAtomsChannels());
 const Observable::channels_t GLMoleculeObject_molecule::HullChannels(getAllAtomicChangesChannels());
-const Observable::channels_t GLMoleculeObject_molecule::BoundingBoxChannels(getAllAtomicChangesChannels());
+const Observable::channels_t GLMoleculeObject_molecule::BoundingBoxChannels(1, molecule::BoundingBoxChanged);
 const Observable::channels_t GLMoleculeObject_molecule::IndexChannels(1, molecule::IndexChanged);
 const Observable::channels_t GLMoleculeObject_molecule::NameChannels(1, molecule::MoleculeNameChanged);
@@ -403 +403 @@
 }
 
-GLMoleculeObject_molecule::BoundingBoxInfo GLMoleculeObject_molecule::initBoundingBox() const
-{
-  BoundingBoxInfo info;
+molecule::BoundingBoxInfo GLMoleculeObject_molecule::initBoundingBox() const
+{
+  molecule::BoundingBoxInfo info;
   info.position = zeroVec;
   info.radius = 0.;
@@ -411 +411 @@
 }
 
-GLMoleculeObject_molecule::BoundingBoxInfo GLMoleculeObject_molecule::updateBoundingBox() const
-{
-  BoundingBoxInfo info = BoundingBox.get();
+molecule::BoundingBoxInfo GLMoleculeObject_molecule::updateBoundingBox() const
+{
+  molecule::BoundingBoxInfo info = BoundingBox.get();
   const molecule * const _molecule = getMolecule(MolIndex.get());
   if (_molecule != NULL) {
@@ -472 +472 @@
 void GLMoleculeObject_molecule::resetBoundingBox()
 {
-  BoundingBoxInfo info = BoundingBox.get();
+  molecule::BoundingBoxInfo info = BoundingBox.get();
   setPosition(QVector3D(info.position[0], info.position[1], info.position[2]));
   setScale(info.radius + 0.3); // getBoundingSphere() only sees atoms as points, so make the box a bit bigger

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp

@@ -24 +24 @@
 #include "GLMoleculeObject_bond.hpp"
 
+#include "molecule.hpp"
+
 class atom;
 class bond;
 class GLMoleculeObject_atom;
 class GLWorldScene;
-class molecule;
 
 class GLMoleculeObject_molecule : public GLMoleculeObject, public Observer
@@ -109 +110 @@
   typedef std::set<atomId_t> atoms_t;
 
-  /** Structure for the required information on the bounding box.
-   *
-   */
-  struct BoundingBoxInfo {
-    //!> position of center
-    Vector position;
-    //!> radius of sphere
-    double radius;
-  };
-
-  /** Structure for the required information on the tesselation hull.
-   *
-   */
-  struct TesselationHullInfo {
-  };
-
-  BoundingBoxInfo initBoundingBox() const;
+  molecule::BoundingBoxInfo initBoundingBox() const;
 
   QGeometryData updateTesselationHull() const;
-  BoundingBoxInfo updateBoundingBox() const;
+  molecule::BoundingBoxInfo updateBoundingBox() const;
   atoms_t updateAtoms();
   moleculeId_t updateIndex() const;
@@ -153 +138 @@
   boost::function<std::string ()> MolNameUpdater;
   boost::function<QGeometryData ()> TesselationHullUpdater;
-  boost::function<BoundingBoxInfo ()> BoundingBoxUpdater;
+  boost::function<molecule::BoundingBoxInfo ()> BoundingBoxUpdater;
   boost::function<atoms_t ()> PresentAtomsUpdater;
 
@@ -163 +148 @@
   Cacheable<QGeometryData> TesselationHull;
   //!> contains newest version of the bounding box on request
-  ObservedValue<BoundingBoxInfo> BoundingBox;
+  ObservedValue<molecule::BoundingBoxInfo> BoundingBox;
   //!> contains the current live set of atoms for the molecule
   ObservedValue<atoms_t> PresentAtoms;

src/World.cpp

@@ -396 +396 @@
   if (isAtomSelected(id))
     selectedAtoms.erase(id);
+  DeleteAtom(atom);
   atoms.erase(id);
-  DeleteAtom(atom);
   atomIdPool.releaseId(id);
   // remove molecule if empty

src/molecule.cpp

@@ -36 +36 @@
 
 #include <algorithm>
+#include <boost/assign.hpp>
 #include <boost/bind.hpp>
 #include <boost/foreach.hpp>
@@ -50 +51 @@
 #include "CodePatterns/enumeration.hpp"
 #include "CodePatterns/Log.hpp"
+#include "CodePatterns/Observer/Observable.hpp"
 #include "CodePatterns/Observer/Notification.hpp"
 #include "config.hpp"
@@ -67 +69 @@
 #include "WorldTime.hpp"
 
+using namespace boost::assign;
+
+// static entities
+static Observable::channels_t getBoundingBoxChannels()
+{
+  Observable::channels_t channels;
+  channels += molecule::AtomInserted, molecule::AtomRemoved, molecule::AtomMoved;
+  return channels;
+}
 
 /************************************* Functions for class molecule *********************************/
@@ -83 +94 @@
   BondCount(this,boost::bind(&molecule::doCountBonds,this),"BondCount"),
   atomIdPool(1, 20, 100),
+  BoundingBoxSweepingAxis(std::vector<AtomDistanceMap_t>(NDIM)),
   _lastchangedatomid(-1),
   last_atom(0)
@@ -92 +104 @@
     OurChannel->addChannel(type);
 
+  // cannot initialize in initializer body as then channels have not been setup yet
+  BoundingBox.reset(
+      new Cacheable<BoundingBoxInfo>(
+          this, boost::bind(&molecule::updateBoundingBox, boost::cref(this)), "molecule_BoundingBox", getBoundingBoxChannels()));
+
   strcpy(name,World::getInstance().getDefaultName().c_str());
-};
+}
 
 molecule *NewMolecule(){
@@ -177 +194 @@
   atomIds.erase( oldId );
   atomIds.insert( newId );
+  // also update BoundingBoxSweepingAxis
+  for (int i=0;i<NDIM;++i) {
+    AtomDistanceMap_t::left_iterator iter = BoundingBoxSweepingAxis[i].left.find(oldId);
+    ASSERT(iter != BoundingBoxSweepingAxis[i].left.end(),
+        "molecule::changeAtomId() - could not find atom "+toString(oldId)
+        +" in BoundingBoxSweepingAxis.");
+    const double component = iter->second;
+    BoundingBoxSweepingAxis[i].left.erase(iter);
+    BoundingBoxSweepingAxis[i].left.insert( std::make_pair(newId, component) );
+  }
   return true;
 }
@@ -237 +264 @@
   atomIds.erase( _atom->getId() );
   {
+    BoundingBoxInfo oldinfo = updateBoundingBox();
+    for (int i=0;i<NDIM;++i)
+      BoundingBoxSweepingAxis[i].left.erase( _atom->getId() );
+    BoundingBoxInfo newinfo = updateBoundingBox();
+    if (oldinfo != newinfo)
+      NOTIFY(BoundingBoxChanged);
+  }
+  {
     NOTIFY(AtomNrChanged);
     atomIdPool.releaseId(_atom->getNr());
@@ -250 +285 @@
 molecule::const_iterator molecule::erase( atom * key )
 {
-  OBSERVE;
-  {
-    _lastchangedatomid = key->getId();
-    NOTIFY(AtomRemoved);
-  }
   const_iterator iter = const_cast<const molecule &>(*this).find(key);
-  if (iter != const_cast<const molecule &>(*this).end()){
-    ++iter;
-    atomIds.erase( key->getId() );
-    {
-      NOTIFY(AtomNrChanged);
-      atomIdPool.releaseId(key->getNr());
-      LocalToGlobalId.erase(key->getNr());
-      key->setNr(-1);
-    }
-    NOTIFY(FormulaChanged);
-    formula-=key->getType();
-    key->removeFromMolecule();
-  }
-  return iter;
+  if (iter != const_cast<const molecule &>(*this).end())
+    return erase(iter);
+  else
+    return iter;
 }
 
@@ -279 +299 @@
   std::pair<iterator,bool> res = atomIds.insert(key->getId());
   if (res.second) { // push atom if went well
+    {
+      BoundingBoxInfo oldinfo = updateBoundingBox();
+      for (int i=0;i<NDIM;++i)
+        BoundingBoxSweepingAxis[i].left.insert( std::make_pair(key->getId(), key->getPosition()[i]));
+      BoundingBoxInfo newinfo = updateBoundingBox();
+      if (oldinfo != newinfo)
+        NOTIFY(BoundingBoxChanged);
+    }
     NOTIFY(AtomNrChanged);
     key->setNr(atomIdPool.getNextId());
@@ -1048 +1076 @@
 }
 
+molecule::BoundingBoxInfo molecule::updateBoundingBox() const
+{
+  BoundingBoxInfo info;
+  Vector min = zeroVec;
+  Vector max = zeroVec;
+  for (int i=0;i<NDIM;++i) {
+    if (!BoundingBoxSweepingAxis[i].right.empty()) {
+      min[i] = BoundingBoxSweepingAxis[i].right.begin()->first;
+      max[i] = BoundingBoxSweepingAxis[i].right.rbegin()->first;
+    }
+  }
+  info.radius = (.5*(max-min)).Norm();
+  info.position = .5*(max+min);
+  return info;
+}
+
+molecule::BoundingBoxInfo molecule::getBoundingBox() const
+{
+  return **BoundingBox;
+}
+
 void molecule::update(Observable *publisher)
 {
@@ -1067 +1116 @@
         // emit others about one of our atoms moved
         _lastchangedatomid = _atom->getId();
+        // update entry in map
+        BoundingBoxInfo oldinfo = updateBoundingBox();
+        for (int i=0;i<NDIM;++i) {
+          AtomDistanceMap_t::left_iterator iter = BoundingBoxSweepingAxis[i].left.find(_atom->getId());
+          ASSERT(iter != BoundingBoxSweepingAxis[i].left.end(),
+              "molecule::recieveNotification() - could not find atom "+toString(_atom->getId())
+              +" in BoundingBoxSweepingAxis.");
+          BoundingBoxSweepingAxis[i].left.erase(iter);
+          BoundingBoxSweepingAxis[i].left.insert(
+              std::make_pair(_atom->getId(), _atom->getPosition()[i]) );
+        }
+        BoundingBoxInfo newinfo = updateBoundingBox();
         OBSERVE;
         NOTIFY(AtomMoved);
+        if (oldinfo != newinfo)
+          NOTIFY(BoundingBoxChanged);
         break;
       }

src/molecule.hpp

@@ -22 +22 @@
 
 #include <string>
+
+#include <boost/bimap/bimap.hpp>
+#include <boost/bimap/unordered_set_of.hpp>
+#include <boost/bimap/multiset_of.hpp>
+#include <boost/optional.hpp>
+#include <boost/shared_ptr.hpp>
 
 #include "AtomIdSet.hpp"
@@ -115 +121 @@
     MoleculeNameChanged,
     IndexChanged,
+    BoundingBoxChanged,
     AboutToBeRemoved,
     NotificationType_MAX
@@ -271 +278 @@
 
 public:
+
+  /** Structure for the required information on the bounding box.
+   *
+   */
+  struct BoundingBoxInfo {
+    //!> position of center
+    Vector position;
+    //!> radius of sphere
+    double radius;
+
+    /** Equivalence operator for bounding box.
+     *
+     * \return true - both bounding boxes have same position and radius
+     */
+    bool operator==(const BoundingBoxInfo &_other) const
+    {  return (radius == _other.radius) && (position == _other.position); }
+
+    /** Inequivalence operator for bounding box.
+     *
+     * \return true - bounding boxes have either different positions or different radii or both
+     */
+    bool operator!=(const BoundingBoxInfo &_other) const
+    { return !(*this == _other); }
+  };
+
+private:
+
+  /** Returns the current bounding box.
+   *
+   * \return Shape with center and extension of box
+   */
+  BoundingBoxInfo updateBoundingBox() const;
+
+  // stuff for keeping bounding box up-to-date efficiently
+
+  //!> Cacheable for the bounding box, ptr such that
+  boost::shared_ptr< Cacheable<BoundingBoxInfo> > BoundingBox;
+  /** Bimap storing atomic ids and the component per axis.
+   *
+   * We need a bimap in order to have the components sorted and be able to
+   * access max and min values in linear time and also access the ids in
+   * constant time in order to update the map, when atoms move, are inserted,
+   * or removed.
+   */
+  typedef boost::bimaps::bimap<
+          boost::bimaps::unordered_set_of< atomId_t >,
+          boost::bimaps::multiset_of< double, std::greater<double> >
+      > AtomDistanceMap_t;
+  std::vector<AtomDistanceMap_t> BoundingBoxSweepingAxis;
+
+public:
+
+  /** Returns the current bounding box of this molecule.
+   *
+   * \return bounding box info with center and radius
+   */
+  BoundingBoxInfo getBoundingBox() const;
 
   /** Function to create a bounding spherical shape for the currently associated atoms.