--- trunk/src/brains/BlockSnapshotManager.cpp	2005/02/16 20:43:10	355
+++ trunk/src/brains/BlockSnapshotManager.cpp	2010/05/10 17:28:26	1442
@@ -6,19 +6,10 @@
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,6 +28,15 @@
  * arising out of the use of or inability to use software, even if the
  * University of Notre Dame has been advised of the possibility of
  * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [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).                        
  */
 #include <algorithm>
 #include "brains/BlockSnapshotManager.hpp"
@@ -46,48 +46,63 @@
 #include "brains/SimInfo.hpp"
 #include "io/DumpReader.hpp"
 
-namespace oopse {
-BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename, 
-    int storageLayout, int blockCapacity) 
+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) {
 
-    nAtoms_ = info->getNGlobalAtoms();
-    nRigidBodies_ = info->getNGlobalRigidBodies();
+      nAtoms_ = info->getNGlobalAtoms();
+      nRigidBodies_ = info->getNGlobalRigidBodies();
 
-    double physMem = physmem_total();
-    double rssMem = residentMem();
-    double avaliablePhysMem = physMem - rssMem;
-    
-    std::cout << "physmem = " << int(physMem) << "\trssMem =  "<< rssMem << "\t availablePhysMem = " << avaliablePhysMem <<std::endl;
-    int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
+      RealType physMem = physmem_total();
+      RealType rssMem = residentMem();
+      RealType avaliablePhysMem = physMem - rssMem;
 
-    int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
-
-    int frameCapacity = int (avaliablePhysMem / bytesPerFrame);
     
-    nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
+      int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
 
-    reader_ = new DumpReader(info, filename);
-    nframes_ = reader_->getNFrames();
+      int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
 
-    int nblocks = nframes_ / nSnapshotPerBlock_;
-    if (nframes_ % nSnapshotPerBlock_ != 0) {
+      // total number of frames that can fit in memory
+      RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
+
+      // number of frames in each block given the need to hold multiple blocks 
+      // in memory at the same time:
+      nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
+      reader_ = new DumpReader(info, filename);
+      nframes_ = reader_->getNFrames();
+      int nblocks = nframes_ / nSnapshotPerBlock_;
+      if (nframes_ % int(nSnapshotPerBlock_) != 0) {
         ++nblocks;
-    }  
+      }  
     
-    for (int i = 0; i < nblocks; ++i) {
+      for (int i = 0; i < nblocks; ++i) {
         blocks_.push_back(SnapshotBlock(i*nSnapshotPerBlock_, (i+1)*nSnapshotPerBlock_));    
-    }
-    //the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
-    blocks_.back().second = nframes_;
+      }
+      //the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
+      blocks_.back().second = nframes_;
 
-    snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));   
+      snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));   
+
+      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;
     
-}
+    }
 
 
-BlockSnapshotManager::~BlockSnapshotManager() {
+  BlockSnapshotManager::~BlockSnapshotManager() {
     currentSnapshot_ = NULL;
     previousSnapshot_ = NULL;
     
@@ -95,13 +110,18 @@ BlockSnapshotManager::~BlockSnapshotManager() {
 
     std::vector<int>::iterator i;
     for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
-        if (*i != -1) {
-            unloadBlock(*i);
-        }
+      if (*i != -1) {
+	unloadBlock(*i);
+      }
     }
-}
+  }
 
-int BlockSnapshotManager::getNActiveBlocks() {
+   Snapshot* BlockSnapshotManager::getSnapshot(int id) { 
+    currentSnapshot_ = snapshots_[id]; 
+    return snapshots_[id]; 
+  }
+
+  int BlockSnapshotManager::getNActiveBlocks() {
 #ifdef __RWSTD   
     int count = 0;
     std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
@@ -109,58 +129,58 @@ int BlockSnapshotManager::getNActiveBlocks() {
 #else
     return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
 #endif
-}
+  }
 
 
 
-bool BlockSnapshotManager::loadBlock(int block) {
+  bool BlockSnapshotManager::loadBlock(int block) {
     std::vector<int>::iterator i = findActiveBlock(block);
     bool loadSuccess;
     if (i != activeBlocks_.end()) {
-        //if block is already in memory, just increast the reference count
-        ++activeRefCount_[i - activeBlocks_.begin()];
-        loadSuccess = true;
+      //if block is already in memory, just increast 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
-        internalLoad(block);
-        loadSuccess = true;
+      //if number of active blocks is less than the block capacity, just load it
+      internalLoad(block);
+      loadSuccess = true;
     } else if (hasZeroRefBlock() > 0) {
-        //if already reach the block capacity, need to unload a block with 0 reference
-        int zeroRefBlock = getFirstZeroRefBlock();
-        assert(zeroRefBlock != -1);
-        internalUnload(zeroRefBlock);
-        internalLoad(block);
+      //if already reach the block capacity, need to unload a block with 0 reference
+      int zeroRefBlock = getFirstZeroRefBlock();
+      assert(zeroRefBlock != -1);
+      internalUnload(zeroRefBlock);
+      internalLoad(block);
     } else {
-        //reach the capacity and all blocks in memory are not zero reference
-        loadSuccess = false;
+      //reach the capacity and all blocks in memory are not zero reference
+      loadSuccess = false;
     }
     
     return loadSuccess;
-}
+  }
 
-bool BlockSnapshotManager::unloadBlock(int block) {
+  bool BlockSnapshotManager::unloadBlock(int block) {
     bool unloadSuccess;
     std::vector<int>::iterator i = findActiveBlock(block);
     
     if (i != activeBlocks_.end()){
-        --activeRefCount_[i - activeBlocks_.begin()];
-        if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
-            //in case, unloadBlock called multiple times
-            activeRefCount_[i - activeBlocks_.begin()]  = 0;
-        }
+      --activeRefCount_[i - activeBlocks_.begin()];
+      if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
+	//in case, unloadBlock called multiple times
+	activeRefCount_[i - activeBlocks_.begin()]  = 0;
+      }
         
-        unloadSuccess = true;
+      unloadSuccess = true;
     } else {
-        unloadSuccess = false;
+      unloadSuccess = false;
     }
 
     return unloadSuccess;
-}
+  }
 
-void BlockSnapshotManager::internalLoad(int block) {
+  void BlockSnapshotManager::internalLoad(int block) {
         
     for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
-        snapshots_[i] = loadFrame(i);
+      snapshots_[i] = loadFrame(i);
     }
     
     std::vector<int>::iterator j;
@@ -168,36 +188,36 @@ void BlockSnapshotManager::internalLoad(int block) {
     assert(j != activeBlocks_.end());
     *j = block;    
     ++activeRefCount_[j - activeBlocks_.begin()];
-}
+  }
 
-void BlockSnapshotManager::internalUnload(int block) {
+  void BlockSnapshotManager::internalUnload(int block) {
     for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
-        delete snapshots_[i];
-        snapshots_[i] = NULL;
+      delete snapshots_[i];
+      snapshots_[i] = NULL;
     }
     std::vector<int>::iterator j;
     j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
     assert(j != activeBlocks_.end());
     *j = -1;
-}
+  }
 
-bool BlockSnapshotManager::hasZeroRefBlock(){
+  bool BlockSnapshotManager::hasZeroRefBlock(){
     return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ?  true : false;
-}
+  }
 
-int BlockSnapshotManager::getFirstZeroRefBlock(){
-     std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
-     return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
-}
+  int BlockSnapshotManager::getFirstZeroRefBlock(){
+    std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
+    return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
+  }
 
-std::vector<int> BlockSnapshotManager::getActiveBlocks() {
+  std::vector<int> BlockSnapshotManager::getActiveBlocks() {
     std::vector<int> result;
-    oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result), 
-        std::bind2nd(std::not_equal_to<int>(), -1));
+    OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result), 
+		   std::bind2nd(std::not_equal_to<int>(), -1));
     return result;    
-}
+  }
 
-Snapshot* BlockSnapshotManager::loadFrame(int frame){
+  Snapshot* BlockSnapshotManager::loadFrame(int frame){
     Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
     snapshot->setID(frame);
     
@@ -205,12 +225,19 @@ Snapshot* BlockSnapshotManager::loadFrame(int frame){
     Snapshot* oldSnapshot = currentSnapshot_;
     currentSnapshot_ = snapshot;   
     reader_->readFrame(frame);
-    currentSnapshot_ = oldSnapshot;
+
+    // What was this for?  It doesn't make sense!
+    //currentSnapshot_ = oldSnapshot;
+
     return snapshot;
-}
+  }
 
-int BlockSnapshotManager::getNFrames() {
+  int BlockSnapshotManager::getNFrames() {
     return reader_->getNFrames();
-}
+  }
 
+  void BlockSnapshotManager::needCOMprops(bool ncp) {
+    reader_->setNeedCOMprops(ncp);
+  }
+
 }