--- trunk/src/brains/SimInfo.cpp	2007/02/26 04:45:42	1121
+++ trunk/src/brains/SimInfo.cpp	2008/04/25 15:14:47	1241
@@ -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;
@@ -155,11 +156,7 @@ namespace oopse {
 	                                        + nGlobalRigidBodies_;
   
       nGlobalMols_ = molStampIds_.size();
-
-#ifdef IS_MPI    
       molToProcMap_.resize(nGlobalMols_);
-#endif
-
     }
 
   SimInfo::~SimInfo() {
@@ -666,6 +663,7 @@ namespace oopse {
     int useSF;
     int useSP;
     int useBoxDipole;
+
     std::string myMethod;
 
     // set the useRF logical
@@ -689,6 +687,8 @@ namespace oopse {
     if (simParams_->haveAccumulateBoxDipole()) 
       if (simParams_->getAccumulateBoxDipole())
 	useBoxDipole = 1;
+
+    useAtomicVirial_ = simParams_->getUseAtomicVirial();
 
     //loop over all of the atom types
     for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
@@ -767,6 +767,9 @@ 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 +789,7 @@ 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() {
@@ -852,25 +856,26 @@ namespace oopse {
     int nGlobalExcludes = 0;
     int* globalExcludes = NULL; 
     int* excludeList = exclude_.getExcludeList();
-    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , 
-		   &nGlobalExcludes, globalExcludes, &molMembershipArray[0], 
-		   &mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); 
-
+    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], 
+                   &nExclude, excludeList , &nGlobalExcludes, globalExcludes, 
+                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_, 
+                   &fortranGlobalGroupMembership[0], &isError); 
+    
     if( isError ){
-
+      
       sprintf( painCave.errMsg,
 	       "There was an error setting the simulation information in fortran.\n" );
       painCave.isFatal = 1;
       painCave.severity = OOPSE_ERROR;
       simError();
     }
-
-#ifdef IS_MPI
+    
+    
     sprintf( checkPointMsg,
 	     "succesfully sent the simulation information to fortran.\n");
-    MPIcheckPoint();
-#endif // is_mpi
-
+    
+    errorCheckPoint();
+    
     // Setup number of neighbors in neighbor list if present
     if (simParams_->haveNeighborListNeighbors()) {
       int nlistNeighbors = simParams_->getNeighborListNeighbors();
@@ -881,9 +886,8 @@ namespace oopse {
   }
 
 
-#ifdef IS_MPI
   void SimInfo::setupFortranParallel() {
-    
+#ifdef IS_MPI    
     //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
     std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
     std::vector<int> localToGlobalCutoffGroupIndex;
@@ -933,13 +937,11 @@ namespace oopse {
     }
 
     sprintf(checkPointMsg, " mpiRefresh successful.\n");
-    MPIcheckPoint();
+    errorCheckPoint();
 
-
+#endif
   }
 
-#endif
-
   void SimInfo::setupCutoff() {           
     
     ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
@@ -947,6 +949,10 @@ namespace oopse {
     // Check the cutoff policy
     int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
 
+    // Set LJ shifting bools to false
+    ljsp_ = false;
+    ljsf_ = false;
+
     std::string myPolicy;
     if (forceFieldOptions_.haveCutoffPolicy()){
       myPolicy = forceFieldOptions_.getCutoffPolicy();
@@ -1010,8 +1016,18 @@ namespace oopse {
 	  simError();
 	}
       }
-      
-      notifyFortranCutoffs(&rcut_, &rsw_);
+
+      if (simParams_->haveElectrostaticSummationMethod()) {
+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
+	toUpper(myMethod);
+        
+	if (myMethod == "SHIFTED_POTENTIAL") {
+	  ljsp_ = true;
+	} else if (myMethod == "SHIFTED_FORCE") {
+	  ljsf_ = true;
+	}
+      }
+      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
       
     } else {
       
@@ -1028,7 +1044,15 @@ namespace oopse {
         if (simParams_->haveElectrostaticSummationMethod()) {
           std::string myMethod = simParams_->getElectrostaticSummationMethod();
           toUpper(myMethod);
-          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
+      
+      // For the time being, we're tethering the LJ shifted behavior to the
+      // electrostaticSummationMethod keyword options
+	  if (myMethod == "SHIFTED_POTENTIAL") {
+	    ljsp_ = true;
+	  } else if (myMethod == "SHIFTED_FORCE") {
+	    ljsf_ = true;
+	  }
+	  if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
             if (simParams_->haveSwitchingRadius()){
               sprintf(painCave.errMsg,
                       "SimInfo Warning: A value was set for the switchingRadius\n"
@@ -1051,7 +1075,9 @@ namespace oopse {
           simError();
           rsw_ = 0.85 * rcut_;
         }
-        notifyFortranCutoffs(&rcut_, &rsw_);
+
+        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
+
       } else {
         // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
         // We'll punt and let fortran figure out the cutoffs later.