--- branches/new_design/OOPSE-3.0/src/brains/SimInfo.cpp	2004/11/15 18:02:15	1739
+++ branches/new_design/OOPSE-3.0/src/brains/SimInfo.cpp	2004/11/30 19:58:25	1804
@@ -33,15 +33,18 @@
 #include <algorithm>
 
 #include "brains/SimInfo.hpp"
+#include "primitives/Molecule.hpp"
+#include "UseTheForce/notifyCutoffs_interface.h"
 #include "utils/MemoryUtils.hpp"
+#include "utils/simError.h"
 
 namespace oopse {
 
-SimInfo::SimInfo(const std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, 
+SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, 
                                 ForceField* ff, Globals* globals) : 
                                 forceField_(ff), globals_(globals), nAtoms_(0), nBonds_(0), 
                                 nBends_(0), nTorsions_(0), nRigidBodies_(0), nIntegrableObjects_(0), 
-                                nCutoffGroups_(0), nConstraints_(0), nZConstraint_(0), sman_(NULL),
+                                nCutoffGroups_(0), nConstraints_(0), nZconstraint_(0), sman_(NULL),
                                 fortranInitialized_(false) {
 
     std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
@@ -63,8 +66,6 @@ SimInfo::SimInfo(const std::vector<std::pair<MoleculeS
     
     nGroups = 0;
     nCutoffAtoms = 0;
-
-    nRigidBodies
     nRigidBodies = 0;
     
     for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
@@ -239,7 +240,7 @@ void SimInfo::calcNdf() {
 
     // nZconstraints_ is global, as are the 3 COM translations for the 
     // entire system:
-    ndf_ = ndf_ - 3 - nZconstraints_;
+    ndf_ = ndf_ - 3 - nZconstraint_;
 
 }
 
@@ -290,7 +291,7 @@ void SimInfo::calcNdfTrans() {
     ndfTrans_ = ndfTrans_local;
 #endif
 
-    ndfTrans_ = ndfTrans_ - 3 - nZconstraints_;
+    ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
  
 }
 
@@ -322,7 +323,7 @@ void SimInfo::addExcludePairs(Molecule* mol) {
         exclude_.addPair(b, c);        
     }
 
-    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
+    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
         a = torsion->getAtomA()->getGlobalIndex();
         b = torsion->getAtomB()->getGlobalIndex();        
         c = torsion->getAtomC()->getGlobalIndex();        
@@ -367,7 +368,7 @@ void SimInfo::removeExcludePairs(Molecule* mol) {
         exclude_.removePair(b, c);        
     }
 
-    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
+    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
         a = torsion->getAtomA()->getGlobalIndex();
         b = torsion->getAtomB()->getGlobalIndex();        
         c = torsion->getAtomC()->getGlobalIndex();        
@@ -391,7 +392,7 @@ void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp
     curStampId = molStampIds_.size();
 
     moleculeStamps_.push_back(molStamp);
-    molStampIds_.insert(molStampIds_.end(), nmol, curStampId)
+    molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
 }
 
 void SimInfo::update() {
@@ -425,9 +426,9 @@ std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
 }
 
 std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
-    typename SimInfo::MoleculeIterator mi;
+    SimInfo::MoleculeIterator mi;
     Molecule* mol;
-    typename Molecule::AtomIterator ai;
+    Molecule::AtomIterator ai;
     Atom* atom;
     std::set<AtomType*> atomTypes;
 
@@ -465,15 +466,15 @@ void SimInfo::setupSimType() {
 
     //loop over all of the atom types
     for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
-        useLennardJones |= i->isLennardJones();
-        useElectrostatic |= i->isElectrostatic();
-        useEAM |= i->isEAM();
-        useCharge |= i->isCharge();
-        useDirectional |= i->isDirectional();
-        useDipole |= i->isDipole();
-        useGayBerne |= i->isGayBerne();
-        useSticky |= i->isSticky();
-        useShape |= i->isShape(); 
+        useLennardJones |= (*i)->isLennardJones();
+        useElectrostatic |= (*i)->isElectrostatic();
+        useEAM |= (*i)->isEAM();
+        useCharge |= (*i)->isCharge();
+        useDirectional |= (*i)->isDirectional();
+        useDipole |= (*i)->isDipole();
+        useGayBerne |= (*i)->isGayBerne();
+        useSticky |= (*i)->isSticky();
+        useShape |= (*i)->isShape(); 
     }
 
     if (useSticky || useDipole || useGayBerne || useShape) {
@@ -539,7 +540,18 @@ void SimInfo::setupSimType() {
     fInfo_.SIM_uses_RF = useRF;
 
     if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
-        fInfo_.dielect = dielectric;
+
+        if (globals_->haveDielectric()) {
+            fInfo_.dielect = globals_->getDielectric();
+        } else {
+            sprintf(painCave.errMsg,
+                    "SimSetup Error: No Dielectric constant was set.\n"
+                    "\tYou are trying to use Reaction Field without"
+                    "\tsetting a dielectric constant!\n");
+            painCave.isFatal = 1;
+            simError();
+        }
+        
     } else {
         fInfo_.dielect = 0.0;
     }
@@ -561,11 +573,11 @@ void SimInfo::setupFortranSim() {
 
     //calculate mass ratio of cutoff group
     std::vector<double> mfact;
-    typename SimInfo::MoleculeIterator mi;
+    SimInfo::MoleculeIterator mi;
     Molecule* mol;
-    typename Molecule::CutoffGroupIterator ci;
+    Molecule::CutoffGroupIterator ci;
     CutoffGroup* cg;
-    typename Molecule::AtomIterator ai;
+    Molecule::AtomIterator ai;
     Atom* atom;
     double totalMass;
 
@@ -606,9 +618,11 @@ void SimInfo::setupFortranSim() {
     //gloalExcludes and molMembershipArray should go away (They are never used)
     //why the hell fortran need to know molecule?
     //OOPSE = Object-Obfuscated Parallel Simulation Engine
-    
-    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, exclude_->getExcludeList(), 
-                  &nGlobalExcludes, globalExcludes, molMembershipArray, 
+    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); 
 
     if( isError ){
@@ -634,9 +648,9 @@ void SimInfo::setupFortranParallel() {
     //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
     std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
     std::vector<int> localToGlobalCutoffGroupIndex;
-    typename SimInfo::MoleculeIterator mi;
-    typename Molecule::AtomIterator ai;
-    typename Molecule::CutoffGroupIterator ci;
+    SimInfo::MoleculeIterator mi;
+    Molecule::AtomIterator ai;
+    Molecule::CutoffGroupIterator ci;
     Molecule* mol;
     Atom* atom;
     CutoffGroup* cg;
@@ -690,8 +704,8 @@ double SimInfo::calcMaxCutoffRadius() {
 double SimInfo::calcMaxCutoffRadius() {
 
 
-    std::vector<AtomType*> atomTypes;
-    std::vector<AtomType*>::iterator i;
+    std::set<AtomType*> atomTypes;
+    std::set<AtomType*>::iterator i;
     std::vector<double> cutoffRadius;
 
     //get the unique atom types
@@ -702,7 +716,7 @@ double SimInfo::calcMaxCutoffRadius() {
         cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
     }
 
-    double maxCutoffRadius = std::max_element(cutoffRadius.begin(), cutoffRadius.end());
+    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
 #ifdef IS_MPI
     //pick the max cutoff radius among the processors
 #endif
@@ -752,7 +766,7 @@ void SimInfo::setupCutoff() {
         }
 
         if (globals_->haveRsw()) {
-            rsw_  = globals_->getRsw()
+            rsw_  = globals_->getRsw();
         } else {
             rsw_ = rcut_;
         }