--- trunk/src/integrators/RNEMD.hpp	2009/03/19 21:03:36	1330
+++ branches/development/src/rnemd/RNEMD.hpp	2012/08/07 18:26:40	1773
@@ -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 +28,16 @@
  * 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).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 /**
@@ -51,44 +52,113 @@
 #define INTEGRATORS_RNEMD_HPP
 #include "brains/SimInfo.hpp"
 #include "math/RandNumGen.hpp"
+#include "selection/SelectionEvaluator.hpp"
+#include "selection/SelectionManager.hpp"
+#include <iostream>
 
-namespace oopse {
+using namespace std;
+namespace OpenMD {
 
-  /**
-   * @class RNEMD RNEMD.hpp "integrators/RNEMD.hpp"
-   * @todo document
-   */
   class RNEMD {
   public:
     RNEMD(SimInfo* info);
     virtual ~RNEMD();
-        
+    
+    void doRNEMD();
     void doSwap();
-    void set_RNEMD_swapTime(RealType swapTime) { swapTime_ = swapTime; }
-    void set_RNEMD_nBins(int nbins) { nBins_ = nbins; }
-    RealType get_RNEMD_exchange_total() { return exchangeSum_; }
-    void set_RNEMD_exchange_total(RealType et) {exchangeSum_ = et;}
-        
+    void doNIVS();
+    void doVSS();
+    void collectData();
+    void getStarted();
+    bool inSlabA(Vector3d pos);
+    bool inSlabB(Vector3d pos);
+    void parseOutputFileFormat(const std::string& format);
+    void writeOutputFile();
+    void writeReal(int index, unsigned int bin);
+    void writeVector(int index, unsigned int bin);
+
   private:
-        
-    enum RNEMDTypeEnum {
-      rnemdKinetic,
-      rnemdPx,
-      rnemdPy,
-      rnemdPz,
-      rnemdUnknown
+
+    enum RNEMDMethod {
+      rnemdSwap,
+      rnemdNIVS,
+      rnemdVSS,
+      rnemdUnkownMethod
     };
-     
+    enum RNEMDFluxType {
+      rnemdKE,       // translational kinetic energy flux
+      rnemdRotKE,    // rotational kinetic energy flux
+      rnemdFullKE,   // full kinetic energy flux
+      rnemdPx,       // flux of momentum along x axis 
+      rnemdPy,       // flux of momentum along y axis 
+      rnemdPz,       // flux of momentum along z axis 
+      rnemdPvector,  // flux of momentum vector
+      rnemdKePx,     // flux of translational KE and x-momentum
+      rnemdKePy,     // flux of translational KE and y-momentum
+      rnemdKePvector, // full combo platter
+      rnemdUnknownFluxType
+    };
+
+    enum OutputFields {
+      BEGININDEX = 0,
+      Z = BEGININDEX,
+      TEMPERATURE,
+      VELOCITY,
+      DENSITY,
+      ENDINDEX 
+    };
+
+    struct OutputData {
+      string title;
+      string units;
+      string dataType;
+      vector<Accumulator*> accumulator;
+    };
+
+    typedef bitset<ENDINDEX-BEGININDEX> OutputBitSet;
+    typedef map<string, OutputFields> OutputMapType;
+    
     SimInfo* info_;
-    RandNumGen* randNumGen_;
-    int nBins_;   
-    RealType swapTime_;
-    RealType exchangeSum_;
-    RNEMDTypeEnum rnemdType_;
-    std::map<std::string, RNEMDTypeEnum> stringToEnumMap_;
 
+    map<string, RNEMDMethod> stringToMethod_;
+    map<string, RNEMDFluxType> stringToFluxType_;
+    RNEMDMethod rnemdMethod_;
+    RNEMDFluxType rnemdFluxType_;
+    string rnemdObjectSelection_;
+    SelectionEvaluator evaluator_;
+    SelectionManager seleMan_;
+    bool usePeriodicBoundaryConditions_;
+    int nBins_; 
+    RealType slabWidth_;
+    RealType slabACenter_;
+    RealType slabBCenter_;
 
-  };
+    RealType kineticFlux_;        // target or desired *flux*
+    Vector3d momentumFluxVector_; // target or desired *flux*
 
+    RealType kineticTarget_;     // target or desired one-time exchange energy
+    Vector3d momentumTarget_;    // target or desired one-time exchange momentum
+
+    RealType kineticExchange_;    // actual exchange energy (running total)
+    Vector3d momentumExchange_;   // actual exchange momentum (running total)
+
+    RealType exchangeTime_;
+
+    RealType targetJzpz2_;
+
+    unsigned int trialCount_;
+    unsigned int failTrialCount_;
+    unsigned int failRootCount_;
+
+    string rnemdFileName_;
+    ofstream rnemdFile_;
+
+    RealType runTime_, statusTime_;
+
+    vector<OutputData> data_;
+    OutputBitSet outputMask_;
+    OutputMapType outputMap_;
+
+  };
 }
-#endif //INTEGRATORS_VELOCITIZER_HPP
+#endif //INTEGRATORS_RNEMD_HPP