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

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>
@@ -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(){
@@ -170 +187 @@
 }
 
+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
@@ -227 +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());
@@ -240 +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;
 }
 
@@ -269 +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());
@@ -1038 +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)
 {
@@ -1057 +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;
       }