Changes in src/molecule.cpp [e39e7a:5be798]

File:

• src/molecule.cpp (modified) (11 diffs)

src/molecule.cpp

@@ -36 +36 @@
 
 #include <algorithm>
-#include <boost/assign.hpp>
 #include <boost/bind.hpp>
 #include <boost/foreach.hpp>
@@ -51 +50 @@
 #include "CodePatterns/enumeration.hpp"
 #include "CodePatterns/Log.hpp"
-#include "CodePatterns/Observer/Observable.hpp"
 #include "CodePatterns/Observer/Notification.hpp"
 #include "config.hpp"
@@ -69 +67 @@
 #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 *********************************/
@@ -94 +83 @@
   BondCount(this,boost::bind(&molecule::doCountBonds,this),"BondCount"),
   atomIdPool(1, 20, 100),
-  BoundingBoxSweepingAxis(std::vector<AtomDistanceMap_t>(NDIM)),
   _lastchangedatomid(-1),
   last_atom(0)
@@ -104 +92 @@
     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(){
@@ -187 +170 @@
 }
 
-bool molecule::changeAtomId(int oldId, int newId)
-{
-  OBSERVE;
-  if ((!atomIds.contains( oldId )) || (atomIds.contains( newId )))
-    return false;
-  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;
-}
-
 bool molecule::changeId(moleculeId_t newId){
   // first we move ourselves in the world
@@ -264 +227 @@
   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());
@@ -285 +240 @@
 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())
-    return erase(iter);
-  else
-    return iter;
+  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;
 }
 
@@ -299 +269 @@
   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());
@@ -1076 +1038 @@
 }
 
-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)
 {
@@ -1116 +1057 @@
         // 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;
       }