--- trunk/OOPSE/libmdtools/SimInfo.hpp	2003/09/04 21:48:35	746
+++ trunk/OOPSE/libmdtools/SimInfo.hpp	2004/01/13 23:01:43	941
@@ -30,18 +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
-  unsigned int resetIntegrator; // boolean to reset the integrator
+  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
@@ -56,7 +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.
 
@@ -80,11 +81,14 @@ class SimInfo{ (public)
   int usePBC; // whether we use periodic boundry conditions.
   int useLJ; 
   int useSticky;
-  int useDipole;
+  int useCharges;
+  int useDipoles;
   int useReactionField;
   int useGB;
   int useEAM;
   
+  bool useInitXSstate;
+  double orthoTolerance;
 
   double dt, run_time;           // the time step and total time
   double sampleTime, statusTime; // the position and energy dump frequencies
@@ -96,7 +100,7 @@ class SimInfo{ (public)
   int n_mol;           // n_molecules;
   Molecule* molecules; // the array of molecules
   
-  int nComponents;           // the number of componentsin the system
+  int nComponents;           // the number of components in the system
   int* componentsNmol;       // the number of molecules of each component
   MoleculeStamp** compStamps;// the stamps matching the components
   LinkedMolStamp* headStamp; // list of stamps used in the simulation
@@ -119,9 +123,9 @@ class SimInfo{ (public)
 
   // sets the internal function pointer to fortran.
 
-  void setInternal( void (*fSetup) setFortranSimList, 
-		    void (*fBox) setFortranBoxList, 
-		    void (*fCut) notifyFortranCutOffList ){
+  void setInternal( setFortranSim_TD fSetup,
+		    setFortranBox_TD fBox,
+		    notifyFortranCutOff_TD fCut){
     setFsimulation = fSetup;
     setFortranBoxSize = fBox;
     notifyFortranCutOffs = fCut;
@@ -129,24 +133,27 @@ class SimInfo{ (public)
 
   int getNDF();
   int getNDFraw();
+  int getNDFtranslational();
 
   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 );
+  void setDefaultRcut( double theRcut );
+  void setDefaultEcr( double theEcr );
+  void setDefaultEcr( double theEcr, double theEst );
+  void checkCutOffs( void );
 
   double getRcut( void )  { return rCut; }
   double getRlist( void ) { return rList; }
   double getEcr( void )   { return ecr; }
   double getEst( void )   { return est; }
+  double getMaxCutoff( void ) { return maxCutoff; }
 
   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] );
@@ -158,7 +165,12 @@ 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); 
@@ -172,27 +184,30 @@ class SimInfo{ (public)
 
   SimState* myConfiguration;
 
-  double origRcut, origEcr;
-  int boxIsInit, haveOrigRcut, haveOrigEcr;
+  int boxIsInit, haveRcut, haveEcr;
 
-  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;
+
+  double distXY;
+  double distYZ;
+  double distZX;
+
+
   
   void calcHmatInv( void );
   void calcBoxL();
-  void checkCutOffs( void );
+  double calcMaxCutOff();
 
+
   // private function to initialize the fortran side of the simulation
-  void (*setFsimulation) setFortranSimList;
+  setFortranSim_TD setFsimulation;
 
-  void (*setFortranBoxSize) setFortranBoxList;
+  setFortranBox_TD setFortranBoxSize;
   
-  void (*notifyFortranCutOffs) notifyFortranCutOffList;
+  notifyFortranCutOff_TD notifyFortranCutOffs;
   
   //Addtional Properties of SimInfo
   map<string, GenericData*> properties;