--- trunk/src/brains/BlockSnapshotManager.cpp	2006/05/17 21:51:42	963
+++ branches/development/src/brains/BlockSnapshotManager.cpp	2011/09/14 21:15:17	1629
@@ -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.
@@ -37,40 +28,57 @@
  * 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"
-#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 oopse {
-  BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename, 
-					     int storageLayout, int blockCapacity) 
-    : SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity), 
-      activeBlocks_(blockCapacity_, -1), activeRefCount_(blockCapacity_, 0) {
+namespace OpenMD {
+  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 bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
 
-      int frameCapacity = int (avaliablePhysMem / bytesPerFrame);
-    
-      nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
+      // total number of frames that can fit in memory
+      //RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
+      RealType frameCapacity = memSize_ / 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_ % nSnapshotPerBlock_ != 0) {
+      if (nframes_ % int(nSnapshotPerBlock_) != 0) {
         ++nblocks;
       }  
     
@@ -82,8 +90,20 @@ namespace oopse {
 
       snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));   
 
-      std::cout << "physmem = " << int(physMem) << "\trssMem =  "<< int(rssMem) << "\t availablePhysMem = " << int(avaliablePhysMem) <<std::endl;
-      std::cout << "nSnapshotPerBlock = " << nSnapshotPerBlock_ << "\t total block = " << nblocks << 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;
     
     }
 
@@ -102,6 +122,11 @@ namespace oopse {
     }
   }
 
+   Snapshot* BlockSnapshotManager::getSnapshot(int id) { 
+    currentSnapshot_ = snapshots_[id]; 
+    return snapshots_[id]; 
+  }
+
   int BlockSnapshotManager::getNActiveBlocks() {
 #ifdef __RWSTD   
     int count = 0;
@@ -193,20 +218,23 @@ namespace oopse {
 
   std::vector<int> BlockSnapshotManager::getActiveBlocks() {
     std::vector<int> result;
-    oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result), 
+    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* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
+    Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_, getStorageLayout());
     snapshot->setID(frame);
     
     /** @todo fixed me */
     Snapshot* oldSnapshot = currentSnapshot_;
     currentSnapshot_ = snapshot;   
     reader_->readFrame(frame);
-    currentSnapshot_ = oldSnapshot;
+
+    // What was this for?  It doesn't make sense!
+    //currentSnapshot_ = oldSnapshot;
+
     return snapshot;
   }
 
@@ -214,4 +242,8 @@ namespace oopse {
     return reader_->getNFrames();
   }
 
+  void BlockSnapshotManager::needCOMprops(bool ncp) {
+    reader_->setNeedCOMprops(ncp);
+  }
+
 }