--- branches/new_design/OOPSE-2.0/src/brains/SimInfo.cpp	2004/12/03 21:30:30	1843
+++ branches/new_design/OOPSE-2.0/src/brains/SimInfo.cpp	2004/12/16 19:20:49	1895
@@ -32,13 +32,20 @@
 
 #include <algorithm>
 #include <set>
+
 #include "brains/SimInfo.hpp"
+#include "math/Vector3.hpp"
 #include "primitives/Molecule.hpp"
 #include "UseTheForce/doForces_interface.h"
 #include "UseTheForce/notifyCutoffs_interface.h"
 #include "utils/MemoryUtils.hpp"
 #include "utils/simError.h"
 
+#ifdef IS_MPI
+#include "UseTheForce/mpiComponentPlan.h"
+#include "UseTheForce/DarkSide/simParallel_interface.h"
+#endif 
+
 namespace oopse {
 
 SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, 
@@ -146,6 +153,8 @@ bool SimInfo::addMolecule(Molecule* mol) {
         nCutoffGroups_ += mol->getNCutoffGroups();
         nConstraints_ += mol->getNConstraints();
 
+        addExcludePairs(mol);
+        
         return true;
     } else {
         return false;
@@ -169,6 +178,7 @@ bool SimInfo::removeMolecule(Molecule* mol) {
         nCutoffGroups_ -= mol->getNCutoffGroups();
         nConstraints_ -= mol->getNConstraints();
 
+        removeExcludePairs(mol);
         molecules_.erase(mol->getGlobalIndex());
 
         delete mol;
@@ -379,7 +389,7 @@ void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp
     int curStampId;
 
     //index from 0
-    curStampId = molStampIds_.size();
+    curStampId = moleculeStamps_.size();
 
     moleculeStamps_.push_back(molStamp);
     molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
@@ -452,8 +462,8 @@ void SimInfo::setupSimType() {
     int useDirectionalAtom = 0;    
     int useElectrostatics = 0;
     //usePBC and useRF are from simParams
-    bool usePBC = simParams_->getPBC();
-    bool useRF = simParams_->getUseRF();
+    int usePBC = simParams_->getPBC();
+    int useRF = simParams_->getUseRF();
 
     //loop over all of the atom types
     for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
@@ -602,7 +612,7 @@ void SimInfo::setupFortranSim() {
     //molMembershipArray is filled by SimCreator    
     std::vector<int> molMembershipArray(nGlobalAtoms_);
     for (int i = 0; i < nGlobalAtoms_; i++) {
-        molMembershipArray.push_back(globalMolMembership_[i] + 1);
+        molMembershipArray[i] = globalMolMembership_[i] + 1;
     }
     
     //setup fortran simulation
@@ -670,11 +680,11 @@ void SimInfo::setupFortranParallel() {
     parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
     parallelData.nGroupsLocal = getNCutoffGroups();
     parallelData.myNode = worldRank;
-    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData->nProcessors));
+    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
 
     //pass mpiSimData struct and index arrays to fortran
-    setFsimParallel(parallelData, &(parallelData->nAtomsLocal),
-                    &localToGlobalAtomIndex[0],  &(parallelData->nGroupsLocal),
+    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
+                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
                     &localToGlobalCutoffGroupIndex[0], &isError);
 
     if (isError) {
@@ -831,6 +841,13 @@ Vector3d SimInfo::getComVel(){ 
         comVel += mass * mol->getComVel();
     }  
 
+#ifdef IS_MPI
+    double tmpMass = totalMass;
+    Vector3d tmpComVel(comVel);    
+    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
+    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
+#endif
+
     comVel /= totalMass;
 
     return comVel;
@@ -849,6 +866,13 @@ Vector3d SimInfo::getCom(){ 
         com += mass * mol->getCom();
     }  
 
+#ifdef IS_MPI
+    double tmpMass = totalMass;
+    Vector3d tmpCom(com);    
+    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
+    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
+#endif
+
     com /= totalMass;
 
     return com;