--- trunk/OOPSE/libmdtools/SimInfo.hpp	2003/03/21 17:42:12	378
+++ trunk/OOPSE/libmdtools/SimInfo.hpp	2003/07/01 21:33:45	569
@@ -30,30 +30,53 @@ 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 rRF;             // the reaction field cut off radius
+  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 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 HmatI[9]; // the inverted Hmat;
+  double boxLx, boxLy, boxLz; // the box Lengths
+  double boxVol, orthoRhombic;
+  
+
+
   double rList, rCut; // variables for the neighborlist
   
   int usePBC; // whether we use periodic boundry conditions.
@@ -81,7 +104,7 @@ 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
@@ -102,8 +125,20 @@ class SimInfo{ (public)
     setFortranBoxSize = fBox;
   }
 
+  int getNDF();
+  int getNDFraw();
+
+  void setBox( double newBox[3] );
+  void setBoxM( double newBox[9] );
+  void getBoxM( double theBox[9] );
+
+  void wrapVector( double thePos[3] );
+
 private:
   
+  void calcHmatI( void );
+  void calcBoxL();
+
   // private function to initialize the fortran side of the simulation
   void (*setFsimulation) setFortranSimList;