--- trunk/src/hydrodynamics/Sphere.cpp	2006/05/16 02:06:37	956
+++ branches/development/src/hydrodynamics/Sphere.cpp	2010/07/09 23:08:25	1465
@@ -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.
@@ -37,15 +28,24 @@
  * 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 "hydrodynamics/Sphere.hpp"
-#include "utils/OOPSEConstant.hpp"
+#include "utils/PhysicalConstants.hpp"
 #include "math/LU.hpp"
 
-namespace oopse {
+namespace OpenMD {
   
-  Sphere::Sphere(Vector3d origin, double radius) : origin_(origin), radius_(radius){
+  Sphere::Sphere(Vector3d origin, RealType radius) : origin_(origin), radius_(radius){
     
   }
   
@@ -69,27 +69,30 @@ namespace oopse {
     return boundary;
   }
   
-  HydroProps Sphere::getHydroProps(double viscosity, double temperature) {
-    HydroProps props;
-    props.center =V3Zero;
-    double Xitt  = 6.0 * NumericConstant::PI * viscosity * radius_;
-    double Xirr = 8.0 * NumericConstant::PI * viscosity * radius_ * radius_ * radius_;
-    props.Xi(0, 0) = Xitt;
-    props.Xi(1, 1) = Xitt;
-    props.Xi(2, 2) = Xitt;
-    props.Xi(3, 3) = Xirr;
-    props.Xi(4, 4) = Xirr;
-    props.Xi(5, 5) = Xirr;
+  HydroProp* Sphere::getHydroProp(RealType viscosity, RealType temperature) {
     
-    const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
-    props.Xi *= convertConstant;
-    Mat6x6d XiCopy = props.Xi;
-    invertMatrix(XiCopy, props.D);
-    double kt = OOPSEConstant::kB * temperature;
-    props.D *= kt;
-    props.Xi *= OOPSEConstant::kb * temperature;
+    RealType Xitt  = 6.0 * NumericConstant::PI * viscosity * radius_;
+    RealType Xirr = 8.0 * NumericConstant::PI * viscosity * radius_ * radius_ * radius_;
+
+    Mat6x6d Xi, XiCopy, D;
+
+    Xi(0, 0) = Xitt;
+    Xi(1, 1) = Xitt;
+    Xi(2, 2) = Xitt;
+    Xi(3, 3) = Xirr;
+    Xi(4, 4) = Xirr;
+    Xi(5, 5) = Xirr;
     
-    return props;
+    Xi *= PhysicalConstants::viscoConvert;
+    XiCopy = Xi;
+
+    invertMatrix(XiCopy, D);
+    RealType kt = PhysicalConstants::kb * temperature; // in kcal mol^-1
+    D *= kt;  // now in angstroms^2 fs^-1  (at least for Trans-trans)
+
+    HydroProp* hprop = new HydroProp(V3Zero, Xi, D);
+    
+    return hprop;
   }
   
 }