--- trunk/OOPSE/libmdtools/SimInfo.hpp	2003/06/30 22:04:01	568
+++ trunk/OOPSE/libmdtools/SimInfo.hpp	2003/08/11 18:29:46	674
@@ -1,16 +1,20 @@
 #ifndef __SIMINFO_H__
 #define __SIMINFO_H__
 
+#include <map>
+#include <string>
+#include <vector>
 
-
 #include "Atom.hpp"
 #include "Molecule.hpp"
 #include "AbstractClasses.hpp"
 #include "MakeStamps.hpp"
+#include "SimState.hpp"
 
 #define __C
 #include "fSimulation.h"
 #include "fortranWrapDefines.hpp"
+#include "GenericData.hpp"
 
 
 
@@ -19,7 +23,7 @@ class SimInfo{ (public)
 public:
 
   SimInfo();
-  ~SimInfo(){}
+  ~SimInfo();
 
   int n_atoms; // the number of atoms
   Atom **atoms; // the array of atom objects
@@ -32,14 +36,13 @@ class SimInfo{ (public)
   unsigned int n_oriented; // number of of atoms with orientation
   unsigned int ndf;        // number of actual degrees of freedom
   unsigned int ndfRaw;     // number of settable degrees of freedom
+  unsigned int n_Zconstraints; // the number of zConstraints
 
   unsigned int setTemp;   // boolean to set the temperature at each sampleTime
 
   unsigned int n_dipoles; // number of dipoles
-  double ecr;             // the electrostatic cutoff radius
-  double est;             // the electrostatic skin thickness
-  double dielectric;      // the dielectric of the medium for reaction field
 
+
   int n_exclude;  // the # of pairs excluded from long range forces
   Exclude** excludes;       // the pairs themselves
 
@@ -56,28 +59,22 @@ class SimInfo{ (public)
 
   double lrPot; // the potential energy from the long range calculations.
 
-  double Hmat[9]; // the periodic boundry conditions. The Hmat is the
-                  // column vectors of the x, y, and z box vectors.
-                  // 
-                  //   h1  h2  h3
-                  // [ Xx  Yx  Zx ]
-                  // [ Xy  Yy  Zy ]
-                  // [ Xz  Yz  Zz ]
-                  //   
-                  // to preserve compatibility with Fortran the
-                  // ordering in the array is as follows:
-                  // 
-                  // [ 0 3 6 ]
-                  // [ 1 4 7 ]
-                  // [ 2 5 8 ]
+  double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
+                      // column vectors of the x, y, and z box vectors.
+                      //   h1  h2  h3
+                      // [ Xx  Yx  Zx ]
+                      // [ Xy  Yy  Zy ]
+                      // [ Xz  Yz  Zz ]
+                      //   
+  double HmatInv[3][3];
 
-  double HmatI[9]; // the inverted Hmat;
-  double boxLx, boxLy, boxLz; // the box Lengths
+  double boxL[3]; // The Lengths of the 3 column vectors of Hmat
   double boxVol;
+  int orthoRhombic;
   
 
+  double dielectric;      // the dielectric of the medium for reaction field
 
-  double rList, rCut; // variables for the neighborlist
   
   int usePBC; // whether we use periodic boundry conditions.
   int useLJ; 
@@ -92,6 +89,7 @@ class SimInfo{ (public)
   double sampleTime, statusTime; // the position and energy dump frequencies
   double target_temp;            // the target temperature of the system
   double thermalTime;            // the temp kick interval
+  double currentTime;            // Used primarily for correlation Functions
 
   int n_mol;           // n_molecules;
   Molecule* molecules; // the array of molecules
@@ -120,29 +118,80 @@ class SimInfo{ (public)
   // sets the internal function pointer to fortran.
 
   void setInternal( void (*fSetup) setFortranSimList, 
-		    void (*fBox) setFortranBoxList ){
+		    void (*fBox) setFortranBoxList, 
+		    void (*fCut) notifyFortranCutOffList ){
     setFsimulation = fSetup;
     setFortranBoxSize = fBox;
+    notifyFortranCutOffs = fCut;
   }
 
   int getNDF();
   int getNDFraw();
 
   void setBox( double newBox[3] );
-  void setBoxM( double newBox[9] );
-  void getBoxM( double theBox[9] );
+  void setBoxM( double newBox[3][3] );
+  void getBoxM( double theBox[3][3] );
+  void scaleBox( double scale );
+  
+  void setRcut( double theRcut );
+  void setEcr( double theEcr );
+  void setEcr( double theEcr, double theEst );
 
+  double getRcut( void )  { return rCut; }
+  double getRlist( void ) { return rList; }
+  double getEcr( void )   { return ecr; }
+  double getEst( void )   { return est; }
+
+  void setTime( double theTime ) { currentTime = theTime; }
+  void incrTime( double dt ) { currentTime += dt; }
+  void decrTime( double dt ) { currentTime -= dt; }
+  double getTime( void ) { return currentTime; }
+
   void wrapVector( double thePos[3] );
 
+  void matMul3(double a[3][3], double b[3][3], double out[3][3]);
+  void matVecMul3(double m[3][3], double inVec[3], double outVec[3]);
+  void invertMat3(double in[3][3], double out[3][3]);
+  void transposeMat3(double in[3][3], double out[3][3]);
+  void printMat3(double A[3][3]);
+  void printMat9(double A[9]);
+  double matDet3(double m[3][3]);
+
+  SimState* getConfiguration( void ) { return myConfiguration; }
+  
+  void addProperty(GenericData* prop); 
+  GenericData* getProperty(const string& propName);
+  vector<GenericData*> getProperties();       
+
 private:
+
+  SimState* myConfiguration;
+
+  double origRcut, origEcr;
+  int boxIsInit, haveOrigRcut, haveOrigEcr;
+
+  double oldEcr;
+  double oldRcut;
+
+  double rList, rCut; // variables for the neighborlist
+  double ecr;             // the electrostatic cutoff radius
+  double est;             // the electrostatic skin thickness
+  double maxCutoff;
   
-  void calcHmatI( void );
+  void calcHmatInv( void );
   void calcBoxL();
+  void checkCutOffs( void );
 
   // private function to initialize the fortran side of the simulation
   void (*setFsimulation) setFortranSimList;
 
   void (*setFortranBoxSize) setFortranBoxList;
+  
+  void (*notifyFortranCutOffs) notifyFortranCutOffList;
+  
+  //Addtional Properties of SimInfo
+  map<string, GenericData*> properties;
+
 };