--- trunk/OOPSE/libmdtools/SimInfo.hpp	2003/03/24 21:55:34	394
+++ trunk/OOPSE/libmdtools/SimInfo.hpp	2003/07/22 16:41:08	644
@@ -30,33 +30,47 @@ class SimInfo{ (public)
   unsigned int n_bends;    // number of bends
   unsigned int n_torsions; // number of torsions
   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 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
-  int *excludes;       // the pairs themselves
+  Exclude** excludes;       // the pairs themselves
 
   int nGlobalExcludes;
   int* globalExcludes; // same as above, but these guys participate in
 		       // no long range forces.
 
   int* identArray;     // array of unique identifiers for the atoms
+  int* molMembershipArray;  // map of atom numbers onto molecule numbers
 
   int n_constraints; // the number of constraints on the system
 
   unsigned int n_SRI;   // the number of short range interactions
-  SRI **sr_interactions;// the array of short range force objects
 
   double lrPot; // the potential energy from the long range calculations.
 
-  double box_x, box_y, box_z; // the periodic boundry conditions
-  double rList, rCut; // variables for the neighborlist
+  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 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
+
+  
   int usePBC; // whether we use periodic boundry conditions.
   int useLJ; 
   int useSticky;
@@ -70,6 +84,7 @@ 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
@@ -82,7 +97,7 @@ class SimInfo{ (public)
   
   char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
   char mixingRule[100]; // the mixing rules for Lennard jones/van der walls 
-  Integrator *the_integrator; // the integrator of the simulation
+  BaseIntegrator *the_integrator; // the integrator of the simulation
 
   char finalName[300];  // the name of the eor file to be written
   char sampleName[300]; // the name of the dump file to be written
@@ -98,17 +113,69 @@ 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[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]);
+  
 private:
+
+  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 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;
+
 };