--- trunk/src/brains/SimInfo.cpp	2006/12/05 00:17:24	1095
+++ trunk/src/brains/SimInfo.cpp	2007/04/06 21:53:43	1126
@@ -92,7 +92,8 @@ namespace oopse {
     nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
     nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
     nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
-    sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
+    sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false), 
+    useAtomicVirial_(true) {
 
       MoleculeStamp* molStamp;
       int nMolWithSameStamp;
@@ -666,6 +667,7 @@ namespace oopse {
     int useSF;
     int useSP;
     int useBoxDipole;
+
     std::string myMethod;
 
     // set the useRF logical
@@ -690,6 +692,8 @@ namespace oopse {
       if (simParams_->getAccumulateBoxDipole())
 	useBoxDipole = 1;
 
+    useAtomicVirial_ = simParams_->getUseAtomicVirial();
+
     //loop over all of the atom types
     for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
       useLennardJones |= (*i)->isLennardJones();
@@ -767,6 +771,9 @@ namespace oopse {
     temp = useBoxDipole;
     MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); 
 
+    temp = useAtomicVirial_;
+    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); 
+
 #endif
 
     fInfo_.SIM_uses_PBC = usePBC;    
@@ -786,6 +793,7 @@ namespace oopse {
     fInfo_.SIM_uses_SF = useSF;
     fInfo_.SIM_uses_SP = useSP;
     fInfo_.SIM_uses_BoxDipole = useBoxDipole;
+    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
   }
 
   void SimInfo::setupFortranSim() {
@@ -873,7 +881,8 @@ namespace oopse {
 
     // Setup number of neighbors in neighbor list if present
     if (simParams_->haveNeighborListNeighbors()) {
-      setNeighbors(simParams_->getNeighborListNeighbors());
+      int nlistNeighbors = simParams_->getNeighborListNeighbors();
+      setNeighbors(&nlistNeighbors);
     }
    
 
@@ -1453,8 +1462,45 @@ namespace oopse {
   
   void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
     IOIndexToIntegrableObject= v;
+  }
+
+  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes 
+     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
+     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to 
+     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
+  */
+  void SimInfo::getGyrationalVolume(RealType &volume){
+    Mat3x3d intTensor;
+    RealType det;
+    Vector3d dummyAngMom; 
+    RealType sysconstants;
+    RealType geomCnst;
+
+    geomCnst = 3.0/2.0;
+    /* Get the inertial tensor and angular momentum for free*/
+    getInertiaTensor(intTensor,dummyAngMom);
+    
+    det = intTensor.determinant();
+    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
+    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
+    return;
   }
 
+  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
+    Mat3x3d intTensor;
+    Vector3d dummyAngMom; 
+    RealType sysconstants;
+    RealType geomCnst;
+
+    geomCnst = 3.0/2.0;
+    /* Get the inertial tensor and angular momentum for free*/
+    getInertiaTensor(intTensor,dummyAngMom);
+    
+    detI = intTensor.determinant();
+    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
+    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
+    return;
+  }
 /*
    void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
       assert( v.size() == nAtoms_ + nRigidBodies_);