--- trunk/src/brains/DataStorage.cpp	2005/04/15 22:04:00	507
+++ trunk/src/brains/DataStorage.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).                        
  */
  
 /**
@@ -49,7 +49,7 @@
 
 #include "brains/DataStorage.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
   DataStorage::DataStorage() : size_(0), storageLayout_(0){
 
@@ -101,7 +101,11 @@ namespace oopse {
       //error
       std::cerr << "size does not match"<< std::endl;        
     }
-
+    if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
+      //error
+      std::cerr << "size does not match"<< std::endl;        
+    }
+    
     return size_;
 
   }
@@ -140,6 +144,10 @@ namespace oopse {
       internalResize(torque, newSize);
     }
 
+    if (storageLayout_ & dslParticlePot) {
+      internalResize(particlePot, newSize);
+    }
+
     size_ = newSize;
   }
 
@@ -175,6 +183,10 @@ namespace oopse {
     if (storageLayout_ & dslTorque) {
       torque.reserve(size);
     }
+    
+    if (storageLayout_ & dslParticlePot) {
+      particlePot.reserve(size);
+    }
 
   }
 
@@ -214,6 +226,10 @@ namespace oopse {
     if (storageLayout_ & dslTorque) {
       internalCopy(torque, source, num, target); 
     }
+
+    if (storageLayout_ & dslParticlePot) {
+      internalCopy(particlePot, source, num, target); 
+    }
     
 
   }
@@ -227,7 +243,7 @@ namespace oopse {
     resize(size_);
   }
 
-  double* DataStorage::getArrayPointer(int whichArray) {
+  RealType* DataStorage::getArrayPointer(int whichArray) {
 
     switch (whichArray) {
     case dslPosition:
@@ -260,7 +276,11 @@ namespace oopse {
 
     case dslTorque:
       return internalGetArrayPointer(torque);
-      break;  
+      break;
+
+    case dslParticlePot:
+      return internalGetArrayPointer(particlePot);
+      break;
             
     default:
       //error message
@@ -269,7 +289,7 @@ namespace oopse {
     }
   }    
 
-  double* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
+  RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
     if (v.size() == 0) {
       return NULL;
     } else {
@@ -277,7 +297,7 @@ namespace oopse {
     }
   }
 
-  double* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
+  RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
     if (v.size() == 0) {
       return NULL;
     } else {
@@ -286,7 +306,7 @@ namespace oopse {
 
   }
 
-  double* DataStorage::internalGetArrayPointer(std::vector<double>& v) {
+  RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
     if (v.size() == 0) {
       return NULL;
     } else {
@@ -338,7 +358,7 @@ namespace oopse {
       bytes += sizeof(Vector3d);
     }
     if (layout & dslAmat) {
-      bytes += sizeof(Mat3x3d);    
+      bytes += sizeof(RotMat3x3d);    
     }
     if (layout & dslAngularMomentum) {
       bytes += sizeof(Vector3d);
@@ -347,7 +367,7 @@ namespace oopse {
       bytes += sizeof(Mat3x3d);
     }
     if (layout & dslZAngle) {
-      bytes += sizeof(Vector3d);
+      bytes += sizeof(RealType);
     }
     if (layout & dslForce) {
       bytes += sizeof(Vector3d);
@@ -355,6 +375,9 @@ namespace oopse {
     if (layout & dslTorque) {
       bytes += sizeof(Vector3d);
     }
+    if (layout & dslParticlePot) {
+      bytes += sizeof(RealType);
+    }
     return bytes;
   }