--- trunk/OOPSE/libmdtools/SimInfo.cpp	2004/05/11 16:00:22	1154
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2004/06/04 03:15:31	1234
@@ -14,6 +14,8 @@ using namespace std;
 
 #include "MatVec3.h"
 
+#include "ConstraintManager.hpp"
+
 #ifdef IS_MPI
 #include "mpiSimulation.hpp"
 #endif
@@ -62,7 +64,11 @@ SimInfo::SimInfo(){
   useReactionField = 0;
   useGB = 0;
   useEAM = 0;
+  useSolidThermInt = 0;
+  useLiquidThermInt = 0;
 
+  haveCutoffGroups = false;
+
   excludes = Exclude::Instance();
 
   myConfiguration = new SimState();
@@ -72,6 +78,8 @@ SimInfo::SimInfo(){
 
   ngroup = 0;
 
+  consMan = NULL;
+  
   wrapMeSimInfo( this );
 }
 
@@ -84,7 +92,9 @@ SimInfo::~SimInfo(){
   
   for(i = properties.begin(); i != properties.end(); i++)
     delete (*i).second;
-  
+
+  if (!consMan)
+    delete consMan;  
 }
 
 void SimInfo::setBox(double newBox[3]) {
@@ -187,7 +197,7 @@ void SimInfo::calcHmatInv( void ) {
 
   if( oldOrtho != orthoRhombic ){
     
-    if( orthoRhombic ){
+    if( orthoRhombic ) {
       sprintf( painCave.errMsg,
 	       "OOPSE is switching from the default Non-Orthorhombic\n"
                "\tto the faster Orthorhombic periodic boundary computations.\n"
@@ -195,6 +205,7 @@ void SimInfo::calcHmatInv( void ) {
                "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
                "\tvariable ( currently set to %G ) smaller.\n",
 	       orthoTolerance);
+      painCave.severity = OOPSE_INFO;
       simError();
     }
     else {
@@ -206,6 +217,7 @@ void SimInfo::calcHmatInv( void ) {
                "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
                "\tvariable ( currently set to %G ) larger.\n",
 	       orthoTolerance);
+      painCave.severity = OOPSE_WARNING;
       simError();
     }
   }
@@ -442,24 +454,27 @@ void SimInfo::refreshSim(){
   excl = excludes->getFortranArray();
   
 #ifdef IS_MPI
-  n_global = mpiSim->getTotAtoms();
+  n_global = mpiSim->getNAtomsGlobal();
 #else
   n_global = n_atoms;
 #endif
   
   isError = 0;
   
-  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
-  
+  getFortranGroupArrays(this, FglobalGroupMembership, mfact);
+  //it may not be a good idea to pass the address of first element in vector
+  //since c++ standard does not require vector to be stored continuously in meomory
+  //Most of the compilers will organize the memory of vector continuously
   setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, 
                   &nGlobalExcludes, globalExcludes, molMembershipArray, 
-                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
-  
+                  &mfact[0], &ngroup, &FglobalGroupMembership[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();
   }
   
@@ -510,6 +525,7 @@ void SimInfo::checkCutOffs( void ){
 	       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.severity = OOPSE_ERROR;
       painCave.isFatal = 1;
       simError();
     }    
@@ -518,6 +534,7 @@ void SimInfo::checkCutOffs( void ){
     sprintf( painCave.errMsg,
              "Trying to check cutoffs without a box.\n"
              "\tOOPSE should have better programmers than that.\n" );
+    painCave.severity = OOPSE_ERROR;
     painCave.isFatal = 1;
     simError();      
   }
@@ -561,67 +578,53 @@ GenericData* SimInfo::getProperty(const string& propNa
 }
 
 
-void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, 
-                          vector<int>& groupList, vector<int>& groupStart){
-  Molecule* mol;
+void SimInfo::getFortranGroupArrays(SimInfo* info, 
+                                    vector<int>& FglobalGroupMembership,
+                                    vector<double>& mfact){
+  
+  Molecule* myMols;
   Atom** myAtoms;
   int numAtom;
-  int curIndex;
   double mtot;
-
+  int numMol;
+  int numCutoffGroups;
+  CutoffGroup* myCutoffGroup;
+  vector<CutoffGroup*>::iterator iterCutoff;
+  Atom* cutoffAtom;
+  vector<Atom*>::iterator iterAtom;
+  int atomIndex;
+  double totalMass;
+  
   mfact.clear();
-  groupList.clear();
-  groupStart.clear();
+  FglobalGroupMembership.clear();
   
-  //Be careful, fortran array begin at 1
-  curIndex = 1;
-  
-  if(info->useMolecularCutoffs){
-    
+
+  // Fix the silly fortran indexing problem
 #ifdef IS_MPI
-    ngroup = mpiSim->getMyNMol();
+  numAtom = mpiSim->getNAtomsGlobal();
 #else
-    ngroup = info->n_mol;
+  numAtom = n_atoms;
 #endif
-    
-    for(int i = 0; i < ngroup; i ++){
-      mol = &(info->molecules[i]);
-      numAtom = mol->getNAtoms();
-      myAtoms = mol->getMyAtoms();
-      mtot = 0.0;
+  for (int i = 0; i < numAtom; i++) 
+    FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
+  
 
-      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);
+  myMols = info->molecules;
+  numMol = info->n_mol;
+  for(int i  = 0; i < numMol; i++){
+    numCutoffGroups = myMols[i].getNCutoffGroups();
+    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); 
+        myCutoffGroup != NULL; 
+        myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
 
-      }
+      totalMass = myCutoffGroup->getMass();
       
-      groupStart.push_back(curIndex);
-      curIndex += numAtom;
-      
-    } //end for(int i =0 ; i < ngroup; i++)    
+      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); 
+          cutoffAtom != NULL; 
+          cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
+        mfact.push_back(cutoffAtom->getMass()/totalMass);
+      }  
+    }
   }
-  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)
-  
+
 }