--- trunk/OOPSE/libmdtools/SimInfo.hpp	2003/08/11 19:38:44	675
+++ trunk/OOPSE/libmdtools/SimInfo.hpp	2003/09/29 21:16:11	790
@@ -30,17 +30,19 @@ class SimInfo{ (public)
   
   double tau[9]; // the stress tensor
 
-  unsigned int n_bonds;    // number of bends
-  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 nZconstraints; // the number of zConstraints
+  int n_bonds;    // number of bends
+  int n_bends;    // number of bends
+  int n_torsions; // number of torsions
+  int n_oriented; // number of of atoms with orientation
+  int ndf;        // number of actual degrees of freedom
+  int ndfRaw;     // number of settable degrees of freedom
+  int ndfTrans;   // number of translational degrees of freedom
+  int nZconstraints; // the number of zConstraints
 
-  unsigned int setTemp;   // boolean to set the temperature at each sampleTime
+  int setTemp;   // boolean to set the temperature at each sampleTime
+  int resetIntegrator; // boolean to reset the integrator
 
-  unsigned int n_dipoles; // number of dipoles
+  int n_dipoles; // number of dipoles
 
 
   int n_exclude;  // the # of pairs excluded from long range forces
@@ -55,7 +57,7 @@ class SimInfo{ (public)
 
   int n_constraints; // the number of constraints on the system
 
-  unsigned int n_SRI;   // the number of short range interactions
+  int n_SRI;   // the number of short range interactions
 
   double lrPot; // the potential energy from the long range calculations.
 
@@ -90,6 +92,7 @@ class SimInfo{ (public)
   double target_temp;            // the target temperature of the system
   double thermalTime;            // the temp kick interval
   double currentTime;            // Used primarily for correlation Functions
+  double resetTime;              // Use to reset the integrator periodically
 
   int n_mol;           // n_molecules;
   Molecule* molecules; // the array of molecules
@@ -108,7 +111,7 @@ class SimInfo{ (public)
   char sampleName[300]; // the name of the dump file to be written
   char statusName[300]; // the name of the stat file to be written
 
-
+  int seed;                    //seed for random number generator
   // refreshes the sim if things get changed (load balanceing, volume
   // adjustment, etc.)
 
@@ -127,6 +130,7 @@ class SimInfo{ (public)
 
   int getNDF();
   int getNDFraw();
+  int getNDFtranslational();
 
   void setBox( double newBox[3] );
   void setBoxM( double newBox[3][3] );
@@ -143,8 +147,8 @@ class SimInfo{ (public)
   double getEst( void )   { return est; }
 
   void setTime( double theTime ) { currentTime = theTime; }
-  void incrTime( double dt ) { currentTime += dt; }
-  void decrTime( double dt ) { currentTime -= dt; }
+  void incrTime( double the_dt ) { currentTime += the_dt; }
+  void decrTime( double the_dt ) { currentTime -= the_dt; }
   double getTime( void ) { return currentTime; }
 
   void wrapVector( double thePos[3] );
@@ -156,13 +160,21 @@ class SimInfo{ (public)
   void printMat3(double A[3][3]);
   void printMat9(double A[9]);
   double matDet3(double m[3][3]);
+  double matTrace3(double m[3][3]);
 
+  void crossProduct3(double a[3],double b[3], double out[3]);
+  double dotProduct3(double a[3], double b[3]);
+  double length3(double a[3]);
+  
   SimState* getConfiguration( void ) { return myConfiguration; }
   
   void addProperty(GenericData* prop); 
   GenericData* getProperty(const string& propName);
   vector<GenericData*> getProperties();       
 
+  int getSeed(void) {  return seed; }
+  void setSeed(int theSeed) {  seed = theSeed;}
+
 private:
 
   SimState* myConfiguration;
@@ -177,9 +189,14 @@ class SimInfo{ (public)
   double ecr;             // the electrostatic cutoff radius
   double est;             // the electrostatic skin thickness
   double maxCutoff;
+
+  double distXY;
+  double distYZ;
+  double distZX;
   
   void calcHmatInv( void );
   void calcBoxL();
+  double calcMaxCutOff();
   void checkCutOffs( void );
 
   // private function to initialize the fortran side of the simulation