--- trunk/src/applications/staticProps/BondOrderParameter.hpp	2006/06/27 16:19:28	994
+++ trunk/src/applications/staticProps/BondOrderParameter.hpp	2012/08/22 02:28:28	1782
@@ -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.
@@ -37,41 +28,102 @@
  * 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] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
+ *  Created by J. Daniel Gezelter on 09/26/06
+ *  @author  J. Daniel Gezelter 
+ *  @version $Id$
+ *
  */
-#ifndef APPLICATIONS_STATICPROPS_P2ORDERPARAMETER_HPP
-#define APPLICATIONS_STATICPROPS_P2ORDERPARAMETER_HPP
+
+#ifndef APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_HPP
+#define APPLICATIONS_STATICPROPS_BONDORDERPARAMETER_HPP
 #include "selection/SelectionEvaluator.hpp"
 #include "selection/SelectionManager.hpp"
 #include "applications/staticProps/StaticAnalyser.hpp"
+#include "math/Vector3.hpp"
+#include "math/SphericalHarmonic.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
-    class P2OrderParameter : public StaticAnalyser{
-        public:
-            P2OrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2);
-            virtual void process();
+  /**
+   * @class BondOrderParameter
+   * @brief Bond Order Parameter
+   *
+   * Computes orientational bond order parameters as outlined in:
+   *
+   *   "Bond-orientaional order in liquids and glasses," by
+   *    P. J. Steinhart, D. R. Nelson, and M. Ronchetti, 
+   *    Phys. Rev. B, 28, 784 (1983).
+   *
+   * A somewhat more useful reference which has formulae for these order
+   * parameters for individual atoms is:
+   *
+   *   "Numerical calculation of the rate of crystal nucleation in a
+   *    Lennard-Jones system at moderate undercooling," by
+   *    Pieter Rein ten Wolde, Maria J. Ruiz-Montero, and Daan Frenkel,
+   *    J. Chem. Phys. 104, pp. 9932-9947 (1996).
+   *
+   * Note that this version uses a single cutoff radius to decide 
+   * membership in the list of neighbors, and does not have use a
+   * distance-dependent weighting as used in the second reference above.
+   *
+   * The selection script can be utilized to look at specific types of
+   * central atoms.  A dynamic selector can also be utilized.  By default, 
+   * this class computes the Q_{l} and \hat{W}_{l} parameters up to l = 12.
+   * The completed configurational averages of these values as
+   * well as the distributions of atomic q_{l} and \hat{w}_{l} values
+   * are then placed in .boq and .bow files.
+   */
+  class BondOrderParameter : public StaticAnalyser{
+  public:
+    BondOrderParameter(SimInfo* info, const std::string& filename, 
+                       const std::string& sele, double rCut, int nbins);
+    
+    virtual ~BondOrderParameter();
+    virtual void process();
+    
+  private:
+    virtual void initalizeHistogram();
+    virtual void collectHistogram(std::vector<RealType> q, 
+                                  std::vector<ComplexType> what);    
+    void writeOrderParameter(std::vector<RealType> Q, 
+                             std::vector<ComplexType> What);
 
-        private:
-
-            struct OrderParam{
-                RealType p2;
-                Vector3d director;
-                RealType angle;
-            };            
-            void writeP2();
-
-            Snapshot* currentSnapshot_;
-
-            std::string selectionScript1_;
-            std::string selectionScript2_;
-            SelectionManager seleMan1_;
-            SelectionManager seleMan2_;       
-            SelectionEvaluator evaluator1_;
-            SelectionEvaluator evaluator2_;
-            std::vector<std::pair<StuntDouble*, StuntDouble*> > sdPairs_;  /**< each pair is used to define a vector, vector = first - second */
-            std::vector<OrderParam> orderParams_;
+    Snapshot* currentSnapshot_;
+    std::string selectionScript_;
+    SelectionManager seleMan_;    
+    SelectionEvaluator evaluator_;           
             
-    };
+    RealType rCut_;
+    static const int lMax_ = 12;
+    int frameCounter_;
+    int nBins_;
+    
+    std::map<std::pair<int,int>,int> m2Min;
+    std::map<std::pair<int,int>,int> m2Max;
+    std::map<std::pair<int,int>,std::vector<RealType> > w3j;
+   
+    RealType MinQ_;
+    RealType MaxQ_;
+    RealType deltaQ_;
+    std::vector<int> Qcount_;
+    std::map<std::pair<int,int>,int> Q_histogram_;
+
+    RealType MinW_;
+    RealType MaxW_;
+    RealType deltaW_;
+    std::vector<int> Wcount_;
+    std::map<std::pair<int,int>,int> W_histogram_;
+  };
 }
 
 #endif