--- trunk/src/primitives/Atom.cpp	2006/05/17 21:51:42	963
+++ trunk/src/primitives/Atom.cpp	2013/06/16 15:15:42	1879
@@ -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.
@@ -37,32 +28,51 @@
  * 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, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
- 
+
+#include "utils/NumericConstant.hpp"
 #include "primitives/Atom.hpp"
-namespace oopse {
+#include "types/FluctuatingChargeAdapter.hpp"
 
-  Atom::Atom(AtomType* at) : StuntDouble(otAtom, &Snapshot::atomData) ,atomType_(at) {
+namespace OpenMD {
+  
+  Atom::Atom(AtomType* at) : StuntDouble(otAtom, &Snapshot::atomData),
+                             atomType_(at) {
     mass_ = at->getMass();
+    if (at->isFluctuatingCharge()) {
+      FluctuatingChargeAdapter fca = FluctuatingChargeAdapter(at);
+      chargeMass_ = fca.getChargeMass();
+    } else {
+      chargeMass_ = NumericConstant::infinity;
+    }
   }
 
   Mat3x3d Atom::getI() {
     return Mat3x3d::identity();
   }    
-
+  
   std::vector<RealType> Atom::getGrad() {
     std::vector<RealType> grad(3);
     Vector3d force= getFrc();
-
+    
     grad[0] = -force[0];
     grad[1] = -force[1];
     grad[2] = -force[2];
     
     return grad;
   }    
-
+  
   void Atom::accept(BaseVisitor* v) {
     v->visit(this);
-  }    
-
+  }      
 }