--- trunk/src/applications/staticProps/SCDOrderParameter.hpp	2005/05/27 21:11:24	545
+++ trunk/src/applications/staticProps/SCDOrderParameter.hpp	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).                        
  */
 #ifndef APPLICATIONS_STATICPROPS_SCDRDERPARAMETER_HPP
 #define APPLICATIONS_STATICPROPS_SCDRDERPARAMETER_HPP
@@ -44,47 +44,48 @@
 #include "selection/SelectionManager.hpp"
 #include "applications/staticProps/StaticAnalyser.hpp"
 #include "utils/Tuple.hpp"
-namespace oopse {
-    class SCDElem {
-        public:
-            SCDElem(SimInfo* info, const std::string& sele1, const std::string& sele2, const std::string& sele3);
+namespace OpenMD {
+  class SCDElem {
+  public:
+    SCDElem(SimInfo* info, const std::string& sele1, const std::string& sele2, const std::string& sele3);
     
-            std::string getSelection1() const {return sele1_;}
-            std::string getSelection2() const {return sele2_;}
-            std::string getSelection3() const {return sele3_;}
-            double calcSCD(Snapshot* snapshot);
+    std::string getSelection1() const {return sele1_;}
+    std::string getSelection2() const {return sele2_;}
+    std::string getSelection3() const {return sele3_;}
+    RealType calcSCD(Snapshot* snapshot);
             
-        private:
+  private:
             
-            std::string sele1_;                
-            std::string sele2_;
-            std::string sele3_;
-
-            typedef tuple3<StuntDouble*, StuntDouble*, StuntDouble*> SDTuple3;
+    std::string sele1_;                
+    std::string sele2_;
+    std::string sele3_;
+    bool usePeriodicBoundaryConditions_;
+      
+    typedef tuple3<StuntDouble*, StuntDouble*, StuntDouble*> SDTuple3;
         
-            std::vector<SDTuple3> tuples_;
-    };
+    std::vector<SDTuple3> tuples_;
+  };
 
 
-    class SCDOrderParameter : public StaticAnalyser{
-        public:
-            SCDOrderParameter(SimInfo* info, const std::string& filename, 
-                const std::string& sele1, const std::string& sele2, const std::string& sele3);
+  class SCDOrderParameter : public StaticAnalyser{
+  public:
+    SCDOrderParameter(SimInfo* info, const std::string& filename, 
+                      const std::string& sele1, const std::string& sele2, const std::string& sele3);
 
-            SCDOrderParameter(SimInfo* info, const std::string& filename, 
-                const std::string& molname, int beginIndex, int endIndex);
-            virtual void process();
+    SCDOrderParameter(SimInfo* info, const std::string& filename, 
+                      const std::string& molname, int beginIndex, int endIndex);
+    virtual void process();
 
-        private:
-            void writeSCD();
+  private:
+    void writeSCD();
 
-            std::vector<SCDElem> scdElems_;
-            std::vector<double> scdParam_;
+    std::vector<SCDElem> scdElems_;
+    std::vector<RealType> scdParam_;
             
-            Snapshot* currentSnapshot_;
+    Snapshot* currentSnapshot_;
 
             
-    };
+  };
 }
 
 #endif