--- trunk/src/hydrodynamics/HydroProp.cpp	2006/06/05 18:24:45	981
+++ branches/development/src/hydrodynamics/HydroProp.cpp	2013/05/17 14:41:42	1875
@@ -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.
@@ -37,25 +28,35 @@
  * 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 "hydrodynamics/HydroProp.hpp"
 #include "utils/StringTokenizer.hpp"
 #include "math/CholeskyDecomposition.hpp"
 
-namespace oopse {
+namespace OpenMD {
   
-  HydroProp::HydroProp(){    
-    hasCOR = false;
-    hasXi = false;
+  HydroProp::HydroProp() : hasCOR(false), hasXi(false) {    
   }
   
-  HydroProp::HydroProp(Vector3d cor, Mat6x6d Xi, Mat6x6d D) : cor_(cor), Xi_(Xi), D_(D){
-    hasCOR = true;
-    hasXi = true;
+  HydroProp::HydroProp(Vector3d cor, Mat6x6d Xi, Mat6x6d D) : cor_(cor), 
+                                                              Xi_(Xi), D_(D), 
+                                                              hasCOR(true), 
+                                                              hasXi(true) {
   }
   
-  HydroProp::HydroProp(const std::string frictionLine) {
+  HydroProp::HydroProp(const std::string &frictionLine) : hasCOR(false),
+                                                          hasXi(false) {
     
     StringTokenizer tokenizer(frictionLine);
     if (tokenizer.countTokens() >= 40) {
@@ -64,6 +65,8 @@ namespace oopse {
       cor_[1] = tokenizer.nextTokenAsDouble();
       cor_[2] = tokenizer.nextTokenAsDouble();
       
+      hasCOR = true;
+
       Xitt_(0,0) = tokenizer.nextTokenAsDouble();
       Xitt_(0,1) = tokenizer.nextTokenAsDouble();
       Xitt_(0,2) = tokenizer.nextTokenAsDouble();
@@ -109,6 +112,8 @@ namespace oopse {
       Xi_.setSubMatrix(3, 0, Xitr_);
       Xi_.setSubMatrix(3, 3, Xirr_);
 
+      hasXi = true;
+
       CholeskyDecomposition(Xi_, S_);            
 
     }