--- trunk/src/brains/SimInfo.hpp	2005/12/02 15:38:03	770
+++ trunk/src/brains/SimInfo.hpp	2006/05/17 21:51:42	963
@@ -75,13 +75,12 @@ namespace oopse{
   class SelectionManager;
   /**
    * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" 
-   * @brief As one of the heavy weight class of OOPSE, SimInfo
-   * One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
-   * And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
-   * cutoff groups, constrains).
-   * Another major change is the index. No matter single version or parallel version,  atoms and
-   * rigid bodies have both global index and local index. Local index is not important to molecule as well as
-   * cutoff group. 
+   * @brief One of the heavy weight classes of OOPSE, SimInfo maintains a list of molecules.
+   * The Molecule class maintains all of the concrete objects 
+   * (atoms, bond, bend, torsions, rigid bodies, cutoff groups, constrains).
+   * In both the  single and parallel versions,  atoms and
+   * rigid bodies have both global and local indices.  The local index is 
+   * not relevant to molecules or cutoff groups.
    */
   class SimInfo {
   public:
@@ -207,7 +206,7 @@ namespace oopse{
 
     /** Returns the number of degrees of freedom */
     int getNdf() {
-      return ndf_;
+      return ndf_ - getFdf();
     }
 
     /** Returns the number of raw degrees of freedom */
@@ -218,8 +217,15 @@ namespace oopse{
     /** Returns the number of translational degrees of freedom */
     int getNdfTrans() {
       return ndfTrans_;
+    }
+
+    /** sets the current number of frozen degrees of freedom */
+    void setFdf(int fdf) {
+      fdf_local = fdf;
     }
 
+    int getFdf(); 
+    
     //getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
         
     /** Returns the total number of z-constraint molecules in the system */
@@ -299,15 +305,15 @@ namespace oopse{
       return i != molecules_.end() ? i->second : NULL;
     }
 
-    double getRcut() {
+    RealType getRcut() {
       return rcut_;
     }
 
-    double getRsw() {
+    RealType getRsw() {
       return rsw_;
     }
 
-    double getList() {
+    RealType getList() {
       return rlist_;
     }
         
@@ -423,7 +429,7 @@ namespace oopse{
         
     friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
 
-    void getCutoff(double& rcut, double& rsw);
+    void getCutoff(RealType& rcut, RealType& rsw);
         
   private:
 
@@ -463,6 +469,8 @@ namespace oopse{
         
     //degress of freedom
     int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
+    int fdf_local;       /**< number of frozen degrees of freedom */
+    int fdf_;            /**< number of frozen degrees of freedom */
     int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
     int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
     int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
@@ -520,9 +528,9 @@ namespace oopse{
     std::string statFileName_;
     std::string restFileName_;
         
-    double rcut_;       /**< cutoff radius*/
-    double rsw_;        /**< radius of switching function*/
-    double rlist_;      /**< neighbor list radius */
+    RealType rcut_;       /**< cutoff radius*/
+    RealType rsw_;        /**< radius of switching function*/
+    RealType rlist_;      /**< neighbor list radius */
 
     bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */