--- trunk/src/brains/SimSnapshotManager.cpp	2005/02/13 06:57:48	318
+++ branches/development/src/brains/SimSnapshotManager.cpp	2010/07/09 23:08:25	1465
@@ -1,4 +1,4 @@
- /*
+/*
  * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
@@ -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.
@@ -37,57 +28,66 @@
  * 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 "brains/SimInfo.hpp"
 #include "brains/SimSnapshotManager.hpp"
 #include "utils/simError.h"
-namespace oopse {
+namespace OpenMD {
 
-SimSnapshotManager::SimSnapshotManager(SimInfo* info, int storageLayout = 255) 
+  SimSnapshotManager::SimSnapshotManager(SimInfo* info, int storageLayout) 
     : SnapshotManager(storageLayout), info_(info){
 
-    int nAtoms = info_->getNAtoms();
-    int nRigidBodies = info_->getNRigidBodies();
+      int nAtoms = info_->getNAtoms();
+      int nRigidBodies = info_->getNRigidBodies();
     
-    //allocate memory for snapshots
-    previousSnapshot_ = new Snapshot(nAtoms, nRigidBodies, storageLayout);
-    currentSnapshot_ = new Snapshot(nAtoms, nRigidBodies, storageLayout);
-}
+      //allocate memory for snapshots
+      previousSnapshot_ = new Snapshot(nAtoms, nRigidBodies, storageLayout);
+      currentSnapshot_ = new Snapshot(nAtoms, nRigidBodies, storageLayout);
+    }
 
-SimSnapshotManager::~SimSnapshotManager(){
+  SimSnapshotManager::~SimSnapshotManager(){
     delete previousSnapshot_;
     delete currentSnapshot_;
     previousSnapshot_ = NULL;
     currentSnapshot_ = NULL;
-}
-bool SimSnapshotManager::advance() {
+  }
+  bool SimSnapshotManager::advance() {
 
     *previousSnapshot_ = *currentSnapshot_;
     currentSnapshot_->setID(currentSnapshot_->getID() + 1);    
     return true;
-}
+  }
 
-Snapshot* SimSnapshotManager::getSnapshot(int id) {
+  Snapshot* SimSnapshotManager::getSnapshot(int id) {
     if (currentSnapshot_ != NULL && currentSnapshot_->getID() == id) {
-        return currentSnapshot_;        
+      return currentSnapshot_;        
     } else if (previousSnapshot_!= NULL && previousSnapshot_->getID() == id) {
-        return previousSnapshot_;
+      return previousSnapshot_;
     } else {
-        return NULL;
+      return NULL;
     }
-}    
+  }    
 
-int SimSnapshotManager::getCapacity() {
+  int SimSnapshotManager::getCapacity() {
     return 2;
-}
+  }
 
-void SimSnapshotManager::setCapacity(int capacity) {
+  void SimSnapshotManager::setCapacity(int capacity) {
     //give warning message
     sprintf( painCave.errMsg,
-        "SimSnapshotManager error: can not set capacity for SimSnapshotManager.\n" );
+	     "SimSnapshotManager error: can not set capacity for SimSnapshotManager.\n" );
     painCave.isFatal = 0;
     simError();    
-}
+  }
 
-} //namespace oopse
+} //namespace OpenMD