--- trunk/OOPSE/libmdtools/SimInfo.cpp	2004/04/20 16:56:40	1127
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2004/05/11 16:00:22	1154
@@ -42,11 +42,10 @@ SimInfo::SimInfo(){
   thermalTime = 0.0;
   currentTime = 0.0;
   rCut = 0.0;
-  ecr = 0.0;
-  est = 0.0;
+  rSw = 0.0;
 
   haveRcut = 0;
-  haveEcr = 0;
+  haveRsw = 0;
   boxIsInit = 0;
   
   resetTime = 1e99;
@@ -71,6 +70,8 @@ SimInfo::SimInfo(){
   has_minimizer = false;
   the_minimizer =NULL;
 
+  ngroup = 0;
+
   wrapMeSimInfo( this );
 }
 
@@ -83,7 +84,7 @@ SimInfo::~SimInfo(){
   
   for(i = properties.begin(); i != properties.end(); i++)
     delete (*i).second;
-    
+  
 }
 
 void SimInfo::setBox(double newBox[3]) {
@@ -439,65 +440,56 @@ void SimInfo::refreshSim(){
 
   n_exclude = excludes->getSize();
   excl = excludes->getFortranArray();
-
+  
 #ifdef IS_MPI
   n_global = mpiSim->getTotAtoms();
 #else
   n_global = n_atoms;
 #endif
-
+  
   isError = 0;
-
+  
+  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
+  
   setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, 
-		  &nGlobalExcludes, globalExcludes, molMembershipArray, 
-                  &isError );
-
+                  &nGlobalExcludes, globalExcludes, molMembershipArray, 
+                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
+  
   if( isError ){
-
+    
     sprintf( painCave.errMsg,
-	     "There was an error setting the simulation information in fortran.\n" );
+             "There was an error setting the simulation information in fortran.\n" );
     painCave.isFatal = 1;
     simError();
   }
-
+  
 #ifdef IS_MPI
   sprintf( checkPointMsg,
 	   "succesfully sent the simulation information to fortran.\n");
   MPIcheckPoint();
 #endif // is_mpi
-
+  
   this->ndf = this->getNDF();
   this->ndfRaw = this->getNDFraw();
   this->ndfTrans = this->getNDFtranslational();
 }
 
 void SimInfo::setDefaultRcut( double theRcut ){
-
+  
   haveRcut = 1;
   rCut = theRcut;
-
-  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
-
-  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
+  rList = rCut + 1.0; 
+  
+  notifyFortranCutOffs( &rCut, &rSw, &rList );
 }
 
-void SimInfo::setDefaultEcr( double theEcr ){
+void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
 
-  haveEcr = 1;
-  ecr = theEcr;
-  
-  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
-
-  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
+  rSw = theRsw;
+  setDefaultRcut( theRcut );
 }
 
-void SimInfo::setDefaultEcr( double theEcr, double theEst ){
 
-  est = theEst;
-  setDefaultEcr( theEcr );
-}
-
-
 void SimInfo::checkCutOffs( void ){
   
   if( boxIsInit ){
@@ -506,42 +498,21 @@ void SimInfo::checkCutOffs( void ){
     
     if( rCut > maxCutoff ){
       sprintf( painCave.errMsg,
-	       "LJrcut is too large for the current periodic box.\n"
-               "\tCurrent Value of LJrcut = %G at time %G\n "
+	       "cutoffRadius is too large for the current periodic box.\n"
+               "\tCurrent Value of cutoffRadius = %G at time %G\n "
                "\tThis is larger than half of at least one of the\n"
                "\tperiodic box vectors.  Right now, the Box matrix is:\n"
-               "\n, %G"
+	       "\n"
 	       "\t[ %G %G %G ]\n"
 	       "\t[ %G %G %G ]\n"
 	       "\t[ %G %G %G ]\n",
-	       rCut, currentTime, maxCutoff,
+	       rCut, currentTime,
 	       Hmat[0][0], Hmat[0][1], Hmat[0][2],
 	       Hmat[1][0], Hmat[1][1], Hmat[1][2],
 	       Hmat[2][0], Hmat[2][1], Hmat[2][2]);
       painCave.isFatal = 1;
       simError();
-    }
-    
-    if( haveEcr ){
-      if( ecr > maxCutoff ){
-	sprintf( painCave.errMsg,
-                 "electrostaticCutoffRadius is too large for the current\n"
-                 "\tperiodic box.\n\n"
-                 "\tCurrent Value of ECR = %G at time %G\n "
-                 "\tThis is larger than half of at least one of the\n"
-                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
-                 "\n"
-                 "\t[ %G %G %G ]\n"
-                 "\t[ %G %G %G ]\n"
-                 "\t[ %G %G %G ]\n",
-		 ecr, currentTime,
-		 Hmat[0][0], Hmat[0][1], Hmat[0][2],
-		 Hmat[1][0], Hmat[1][1], Hmat[1][2],
-		 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
-	painCave.isFatal = 1;
-	simError();
-      }
-    }
+    }    
   } else {
     // initialize this stuff before using it, OK?
     sprintf( painCave.errMsg,
@@ -589,3 +560,68 @@ GenericData* SimInfo::getProperty(const string& propNa
     return NULL;  
 }
 
+
+void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, 
+                          vector<int>& groupList, vector<int>& groupStart){
+  Molecule* mol;
+  Atom** myAtoms;
+  int numAtom;
+  int curIndex;
+  double mtot;
+
+  mfact.clear();
+  groupList.clear();
+  groupStart.clear();
+  
+  //Be careful, fortran array begin at 1
+  curIndex = 1;
+  
+  if(info->useMolecularCutoffs){
+    
+#ifdef IS_MPI
+    ngroup = mpiSim->getMyNMol();
+#else
+    ngroup = info->n_mol;
+#endif
+    
+    for(int i = 0; i < ngroup; i ++){
+      mol = &(info->molecules[i]);
+      numAtom = mol->getNAtoms();
+      myAtoms = mol->getMyAtoms();
+      mtot = 0.0;
+
+      for(int j=0; j < numAtom; j++)
+        mtot += myAtoms[j]->getMass();                
+      
+      for(int j=0; j < numAtom; j++){ 
+               
+        // We want the local Index:
+        groupList.push_back(myAtoms[j]->getIndex() + 1);
+        mfact.push_back(myAtoms[j]->getMass() / mtot);
+
+      }
+      
+      groupStart.push_back(curIndex);
+      curIndex += numAtom;
+      
+    } //end for(int i =0 ; i < ngroup; i++)    
+  }
+  else{
+    //using atomic cutoff, every single atom is just a group
+    
+#ifdef IS_MPI
+    ngroup = mpiSim->getMyNlocal();
+#else
+    ngroup = info->n_atoms;
+#endif
+    
+    for(int i =0 ; i < ngroup; i++){
+      groupStart.push_back(curIndex++);       
+      groupList.push_back((info->atoms[i])->getIndex() + 1);
+      mfact.push_back(1.0);
+      
+    }//end for(int i =0 ; i < ngroup; i++)
+    
+  }//end if (info->useMolecularCutoffs)
+  
+}