--- trunk/src/applications/hydrodynamics/CompositeShape.cpp	2006/03/17 23:20:35	906
+++ trunk/src/applications/hydrodynamics/CompositeShape.cpp	2009/11/25 20:02:06	1390
@@ -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.
@@ -37,54 +28,69 @@
  * 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 "applications/hydrodynamics/CompositeShape.hpp" 
 #include "utils/MemoryUtils.hpp"
 #include "applications/hydrodynamics/HydrodynamicsModel.hpp"
-namespace oopse {
-
-CompositeShape::~CompositeShape() {
+namespace OpenMD {
+  
+  CompositeShape::~CompositeShape() {
     MemoryUtils::deletePointers(shapes_);
-}
-bool CompositeShape::isInterior(Vector3d pos) {
+  }
+  bool CompositeShape::isInterior(Vector3d pos) {
     bool result = false;
     std::vector<Shape*>::iterator iter;
     for (iter = shapes_.begin(); iter != shapes_.end(); ++ iter) {
-        if ((*iter)->isInterior(pos)) {
-            result = true;
-            break;
-        }
+      if ((*iter)->isInterior(pos)) {
+        result = true;
+        break;
+      }
     }
-
+    
     return result;
-}
-
-template<class Cont, class Predict>
-void swap_if(Cont& b1, Cont& b2, Predict predict) {
+  }
+  
+  template<class Cont, class Predict>
+  void swap_if(Cont& b1, Cont& b2, Predict predict) {
     unsigned int size = b1.size();
     assert(size == b2.size());
     for (unsigned int i = 0 ; i < size; ++i) {
-        if (predict(b1[i], b2[i]))
-            std::swap(b1[i], b2[i]);
+      if (predict(b1[i], b2[i]))
+        std::swap(b1[i], b2[i]);
     }
-
-}
-
-std::pair<Vector3d, Vector3d> CompositeShape::getBox() {
+    
+  }
+  
+  std::pair<Vector3d, Vector3d> CompositeShape::getBoundingBox() {
     std::vector<Shape*>::iterator iter = shapes_.begin();
-    std::pair<Vector3d, Vector3d>  boundary = (*iter)->getBox();
+    std::pair<Vector3d, Vector3d>  boundary = (*iter)->getBoundingBox();
     for (++iter; iter != shapes_.end(); ++iter) {
-        std::pair<Vector3d, Vector3d> currBoundary = (*iter)->getBox();
-            swap_if(boundary.first, currBoundary.first, std::less<double>());
-            swap_if(boundary.second, currBoundary.second, std::greater<double>());        
+      std::pair<Vector3d, Vector3d> currBoundary = (*iter)->getBoundingBox();
+      swap_if(boundary.first, currBoundary.first, std::greater<RealType>());
+      swap_if(boundary.second, currBoundary.second, std::less<RealType>());        
     }
-
+    
     return boundary;
+  }
+  
+  HydroProp* CompositeShape::getHydroProp(RealType viscosity, RealType temperature) {
+    HydroProp* props = new HydroProp();
+    props->setCOR(V3Zero);
+    sprintf( painCave.errMsg,
+             "CompositeShape was asked to return an analytic HydroProps.\n");
+    painCave.severity = OPENMD_ERROR;
+    painCave.isFatal = 1;
+    simError();          
+    return props;
+  }   
 }
-
-bool CompositeShape::calcHydroProps(HydrodynamicsModel* model, double viscosity, double temperature) {
-    return model->calcHydroProps(this, viscosity, temperature);
-}
-
-}