--- trunk/src/brains/BlockSnapshotManager.cpp	2013/06/16 15:15:42	1879
+++ trunk/src/brains/BlockSnapshotManager.cpp	2015/03/07 21:41:51	2071
@@ -53,8 +53,9 @@ namespace OpenMD {
 					     int storageLayout,
                                              long long int memSize,
                                              int blockCapacity) 
-    : SnapshotManager(storageLayout), info_(info), memSize_(memSize), 
-      blockCapacity_(blockCapacity), activeBlocks_(blockCapacity_, -1), 
+    : SnapshotManager(storageLayout), info_(info), 
+      blockCapacity_(blockCapacity), memSize_(memSize), 
+      activeBlocks_(blockCapacity_, -1), 
       activeRefCount_(blockCapacity_, 0) {
 
       nAtoms_ = info->getNGlobalAtoms();
@@ -67,8 +68,13 @@ namespace OpenMD {
       // RealType avaliablePhysMem = physMem - rssMem;
     
       int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
-      int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
+      int bytesPerCutoffGroup = DataStorage::getBytesPerStuntDouble(DataStorage::dslPosition);
 
+      int bytesPerFrameData = Snapshot::getFrameDataSize();
+      int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble 
+	+ nCutoffGroups_ * bytesPerCutoffGroup 
+        + bytesPerFrameData;
+
       // total number of frames that can fit in memory
       //RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
       RealType frameCapacity = (RealType) memSize_ / (RealType) bytesPerFrame;
@@ -76,6 +82,9 @@ namespace OpenMD {
       // number of frames in each block given the need to hold multiple blocks 
       // in memory at the same time:
       nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
+      if (nSnapshotPerBlock_ <= 0) {
+       std::cerr << "not enough memory to hold two configs!" << std::endl;
+      }
       reader_ = new DumpReader(info, filename);
       nframes_ = reader_->getNFrames();
       int nblocks = nframes_ / nSnapshotPerBlock_;
@@ -91,20 +100,33 @@ namespace OpenMD {
 
       snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));   
 
-      std::cout << "-----------------------------------------------------"<<std::endl;
+      std::cout << "-----------------------------------------------------"
+                << std::endl;
       std::cout << "BlockSnapshotManager memory report:" << std::endl;
       std::cout << "\n";
       // std::cout << "  Physical Memory available:\t" << (unsigned long)physMem <<  " bytes" <<std::endl;
       //std::cout << "     Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
       //std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
-      std::cout << "Memory requested for OpenMD:\t" << (unsigned long)memSize_ << " bytes" <<std::endl;
-      std::cout << "      Bytes per StuntDouble:\t" << (unsigned long)bytesPerStuntDouble <<std::endl;
-      std::cout << "            Bytes per Frame:\t" << (unsigned long)bytesPerFrame <<std::endl;
-      std::cout << "             Frame Capacity:\t" << (unsigned long)frameCapacity <<std::endl;
-      std::cout << "       Frames in trajectory:\t" << (unsigned long)nframes_ <<std::endl;
-      std::cout << "        Snapshots per Block:\t" << (unsigned long)nSnapshotPerBlock_ <<std::endl;
-      std::cout << "     Total number of Blocks:\t" << (unsigned long)nblocks << std::endl;
-      std::cout << "-----------------------------------------------------"<<std::endl;
+      std::cout << "Memory requested for OpenMD:\t" 
+                << (unsigned long)memSize_ << " bytes" << std::endl;
+      std::cout << "        Bytes per FrameData:\t" 
+                << (unsigned long)bytesPerFrameData << std::endl;
+      std::cout << "      Bytes per StuntDouble:\t" 
+                << (unsigned long)bytesPerStuntDouble << std::endl;
+      std::cout << "     Bytes per Cutoff Group:\t" 
+                << (unsigned long)bytesPerCutoffGroup << std::endl;
+      std::cout << "            Bytes per Frame:\t" 
+                << (unsigned long)bytesPerFrame << std::endl;
+      std::cout << "             Frame Capacity:\t"
+                << (unsigned long)frameCapacity << std::endl;
+      std::cout << "       Frames in trajectory:\t" 
+                << (unsigned long)nframes_ << std::endl;
+      std::cout << "        Snapshots per Block:\t" 
+                << (unsigned long)nSnapshotPerBlock_ << std::endl;
+      std::cout << "     Total number of Blocks:\t" 
+                << (unsigned long)nblocks << std::endl;
+      std::cout << "-----------------------------------------------------"
+                << std::endl;
     
     }
 
@@ -142,26 +164,29 @@ namespace OpenMD {
 
   bool BlockSnapshotManager::loadBlock(int block) {
     std::vector<int>::iterator i = findActiveBlock(block);
-    bool loadSuccess;
+    bool loadSuccess(false);
     if (i != activeBlocks_.end()) {
-      //if block is already in memory, just increast the reference count
+      // If the block is already in memory, just increase the
+      // reference count:
       ++activeRefCount_[i - activeBlocks_.begin()];
       loadSuccess = true;
     } else if (getNActiveBlocks() < blockCapacity_){
-      //if number of active blocks is less than the block capacity, just load it
+      // If the number of active blocks is less than the block
+      // capacity, just load the block:
       internalLoad(block);
       loadSuccess = true;
     } else if ( hasZeroRefBlock() ) {
-      //if already reach the block capacity, need to unload a block with 0 reference
+      // If we have already reached the block capacity, we need to
+      // unload a block with 0 references:
       int zeroRefBlock = getFirstZeroRefBlock();
       assert(zeroRefBlock != -1);
       internalUnload(zeroRefBlock);
       internalLoad(block);
     } else {
-      //reach the capacity and all blocks in memory are not zero reference
+      // We have reached capacity and all blocks in memory are have
+      // non-zero references:
       loadSuccess = false;
-    }
-    
+    }    
     return loadSuccess;
   }
 
@@ -175,6 +200,10 @@ namespace OpenMD {
 	//in case, unloadBlock called multiple times
 	activeRefCount_[i - activeBlocks_.begin()]  = 0;
       }
+
+      if (activeRefCount_[i-activeBlocks_.begin()] == 0) {
+        internalUnload(block);
+      }
         
       unloadSuccess = true;
     } else {
@@ -198,6 +227,7 @@ namespace OpenMD {
   }
 
   void BlockSnapshotManager::internalUnload(int block) {
+    std::cerr << "called internal unload for block "<< block << "\n";
     for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
       delete snapshots_[i];
       snapshots_[i] = NULL;