--- branches/development/src/brains/SimInfo.hpp	2012/05/26 18:13:43	1725
+++ branches/development/src/brains/SimInfo.hpp	2012/10/22 20:42:10	1808
@@ -91,13 +91,9 @@ namespace OpenMD{
     /**
      * Constructor of SimInfo
      *
-     * @param molStampPairs MoleculeStamp Array. The first element of
-     * the pair is molecule stamp, the second element is the total
-     * number of molecules with the same molecule stamp in the system
+     * @param ff pointer to a concrete ForceField instance
      *
-     * @param ff pointer of a concrete ForceField instance
-     *
-     * @param simParams 
+     * @param simParams pointer to the simulation parameters in a Globals object
      */
     SimInfo(ForceField* ff, Globals* simParams);
     virtual ~SimInfo();
@@ -108,7 +104,7 @@ namespace OpenMD{
      * @return return true if adding successfully, return false if the
      * molecule is already in SimInfo
      *
-     * @param mol molecule to be added
+     * @param mol Molecule to be added
      */
     bool addMolecule(Molecule* mol);
 
@@ -233,6 +229,11 @@ namespace OpenMD{
       return ndf_ - getFdf();
     }
 
+    /** Returns the number of degrees of freedom (LOCAL) */
+    int getNdfLocal() {
+      return ndfLocal_;
+    }
+
     /** Returns the number of raw degrees of freedom */
     int getNdfRaw() {
       return ndfRaw_;
@@ -281,29 +282,6 @@ namespace OpenMD{
     Globals* getSimParams() {
       return simParams_;
     }
-
-    /** Returns the velocity of center of mass of the whole system.*/
-    Vector3d getComVel();
-
-    /** Returns the center of the mass of the whole system.*/
-    Vector3d getCom();
-    /** Returns the center of the mass and Center of Mass velocity of
-        the whole system.*/ 
-    void getComAll(Vector3d& com,Vector3d& comVel);
-
-    /** Returns intertia tensor for the entire system and system
-        Angular Momentum.*/
-    void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
-    
-    /** Returns system angular momentum */
-    Vector3d getAngularMomentum();
-
-    /** Returns volume of system as estimated by an ellipsoid defined
-        by the radii of gyration*/
-    void getGyrationalVolume(RealType &vol);
-    /** Overloaded version of gyrational volume that also returns
-        det(I) so dV/dr can be calculated*/
-    void getGyrationalVolume(RealType &vol, RealType &detI);
 
     void update();
     /**
@@ -403,7 +381,6 @@ namespace OpenMD{
 
     /** 
      * Sets GlobalGroupMembership
-     * @see #SimCreator::setGlobalIndex
      */  
     void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
       assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
@@ -412,7 +389,6 @@ namespace OpenMD{
 
     /** 
      * Sets GlobalMolMembership
-     * @see #SimCreator::setGlobalIndex
      */        
     void setGlobalMolMembership(const vector<int>& globalMolMembership) {
       assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
@@ -535,6 +511,7 @@ namespace OpenMD{
        
     /// Degress of freedom
     int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
+    int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
     int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
     int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
     int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
@@ -684,7 +661,6 @@ namespace OpenMD{
     
     /** 
      * Set MolToProcMap array
-     * @see #SimCreator::divideMolecules
      */
     void setMolToProcMap(const vector<int>& molToProcMap) {
       molToProcMap_ = molToProcMap;