--- trunk/src/brains/BlockSnapshotManager.cpp	2010/05/10 17:28:26	1442
+++ trunk/src/brains/BlockSnapshotManager.cpp	2014/01/24 14:17:42	1966
@@ -35,41 +35,55 @@
  *                                                                      
  * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
  * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
- * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
- * [4]  Vardeman & Gezelter, in progress (2009).                        
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
 #include <algorithm>
 #include "brains/BlockSnapshotManager.hpp"
-#include "utils/residentMem.h"
-#include "utils/physmem.h"
+//#include "utils/residentMem.h"
+//#include "utils/physmem.h"
 #include "utils/Algorithm.hpp"
 #include "brains/SimInfo.hpp"
 #include "io/DumpReader.hpp"
 
 namespace OpenMD {
-  BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename, 
-					     int storageLayout, int blockCapacity) 
-    : SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity), 
-      activeBlocks_(blockCapacity_, -1), activeRefCount_(blockCapacity_, 0) {
+  BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, 
+                                             const std::string& filename, 
+					     int storageLayout,
+                                             long long int memSize,
+                                             int blockCapacity) 
+    : SnapshotManager(storageLayout), info_(info), memSize_(memSize), 
+      blockCapacity_(blockCapacity), activeBlocks_(blockCapacity_, -1), 
+      activeRefCount_(blockCapacity_, 0) {
 
       nAtoms_ = info->getNGlobalAtoms();
       nRigidBodies_ = info->getNGlobalRigidBodies();
+      nCutoffGroups_ = info->getNCutoffGroups();
 
-      RealType physMem = physmem_total();
-      RealType rssMem = residentMem();
-      RealType avaliablePhysMem = physMem - rssMem;
-
+      // eliminate suspect calls to figure out free memory:
+      // RealType physMem = physmem_total();
+      // RealType rssMem = residentMem();
+      // RealType avaliablePhysMem = physMem - rssMem;
     
       int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
+      int bytesPerCutoffGroup = DataStorage::getBytesPerStuntDouble(DataStorage::dslPosition);
 
-      int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
+      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 = avaliablePhysMem / bytesPerFrame;
+      RealType frameCapacity = (RealType) memSize_ / (RealType) bytesPerFrame;
 
       // 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_;
@@ -85,19 +99,33 @@ 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 << "      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 << "  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 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;
     
     }
 
@@ -144,7 +172,7 @@ namespace OpenMD {
       //if number of active blocks is less than the block capacity, just load it
       internalLoad(block);
       loadSuccess = true;
-    } else if (hasZeroRefBlock() > 0) {
+    } else if ( hasZeroRefBlock() ) {
       //if already reach the block capacity, need to unload a block with 0 reference
       int zeroRefBlock = getFirstZeroRefBlock();
       assert(zeroRefBlock != -1);
@@ -168,6 +196,10 @@ namespace OpenMD {
 	//in case, unloadBlock called multiple times
 	activeRefCount_[i - activeBlocks_.begin()]  = 0;
       }
+
+      if (activeRefCount_[i-activeBlocks_.begin()] == 0) {
+        internalUnload(block);
+      }
         
       unloadSuccess = true;
     } else {
@@ -191,6 +223,7 @@ 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;
@@ -218,17 +251,14 @@ namespace OpenMD {
   }
 
   Snapshot* BlockSnapshotManager::loadFrame(int frame){
-    Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
+    Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_, 
+                                      getStorageLayout());
     snapshot->setID(frame);
+    snapshot->clearDerivedProperties();
     
-    /** @todo fixed me */
-    Snapshot* oldSnapshot = currentSnapshot_;
     currentSnapshot_ = snapshot;   
     reader_->readFrame(frame);
 
-    // What was this for?  It doesn't make sense!
-    //currentSnapshot_ = oldSnapshot;
-
     return snapshot;
   }