--- trunk/OOPSE/libmdtools/SimInfo.cpp	2004/05/11 21:14:26	1158
+++ 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 +64,9 @@ SimInfo::SimInfo(){
   useReactionField = 0;
   useGB = 0;
   useEAM = 0;
-  
+  useSolidThermInt = 0;
+  useLiquidThermInt = 0;
+
   haveCutoffGroups = false;
 
   excludes = Exclude::Instance();
@@ -74,6 +78,8 @@ SimInfo::SimInfo(){
 
   ngroup = 0;
 
+  consMan = NULL;
+  
   wrapMeSimInfo( this );
 }
 
@@ -86,7 +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]) {
@@ -189,7 +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"
@@ -197,6 +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 {
@@ -208,6 +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();
     }
   }
@@ -444,26 +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 continously in meomory
-  //Most of the compilers will organize the memory of vector continously
+  //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();
   }
   
@@ -514,6 +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();
     }    
@@ -522,6 +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();      
   }
@@ -565,12 +578,13 @@ GenericData* SimInfo::getProperty(const string& propNa
 }
 
 
-void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, 
-                          vector<int>& groupList, vector<int>& groupStart){
+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;
@@ -582,55 +596,35 @@ void getFortranGroupArray(SimInfo* info, vector<double
   double totalMass;
   
   mfact.clear();
-  groupList.clear();
-  groupStart.clear();
+  FglobalGroupMembership.clear();
   
-  //Be careful, fortran array begin at 1
-  curIndex = 1;
+
+  // Fix the silly fortran indexing problem
+#ifdef IS_MPI
+  numAtom = mpiSim->getNAtomsGlobal();
+#else
+  numAtom = n_atoms;
+#endif
+  for (int i = 0; i < numAtom; i++) 
+    FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
+  
 
   myMols = info->molecules;
   numMol = info->n_mol;
   for(int i  = 0; i < numMol; i++){
-    numAtom = myMols[i].getNAtoms();
-    myAtoms = myMols[i].getMyAtoms();
-
-    
-    for(int j = 0; j < numAtom; j++){
-
-    
-#ifdef IS_MPI      
-      atomIndex = myAtoms[j]->getGlobalIndex();
-#else
-      atomIndex = myAtoms[j]->getIndex();
-#endif
-
-      if(myMols[i].belongToCutoffGroup(atomIndex))
-        continue;
-      else{
-        mfact.push_back(myAtoms[j]->getMass());
-        groupList.push_back(myAtoms[j]->getIndex() + 1);
-        groupStart.push_back(curIndex++);   
-      }
-    }
-      
     numCutoffGroups = myMols[i].getNCutoffGroups();
-    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; 
-                                                  myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
+    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); 
+        myCutoffGroup != NULL; 
+        myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
 
       totalMass = myCutoffGroup->getMass();
       
-      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; 
-                                           cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
+      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); 
+          cutoffAtom != NULL; 
+          cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
         mfact.push_back(cutoffAtom->getMass()/totalMass);
-        groupList.push_back(cutoffAtom->getIndex() + 1);
       }  
-                              
-      groupStart.push_back(curIndex);
-      curIndex += myCutoffGroup->getNumAtom();
+    }
+  }
 
-    }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff))
-
-  }//end for(int i  = 0; i < numMol; i++)
-  
-  ngroup = groupStart.size();
 }