--- trunk/OOPSE/libmdtools/mpiSimulation.cpp	2003/10/28 16:03:37	829
+++ trunk/OOPSE/libmdtools/mpiSimulation.cpp	2004/05/27 00:48:12	1198
@@ -17,7 +17,7 @@ mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
   entryPlug = the_entryPlug;
   mpiPlug = new mpiSimData;
   
-  MPI_Comm_size(MPI_COMM_WORLD, &(mpiPlug->numberProcessors) );
+  MPI_Comm_size(MPI_COMM_WORLD, &(mpiPlug->nProcessors) );
   mpiPlug->myNode = worldRank;
 
   MolToProcMap = new int[entryPlug->n_mol];
@@ -40,10 +40,8 @@ mpiSimulation::~mpiSimulation(){
   
 }
 
-int* mpiSimulation::divideLabor( void ){
+void mpiSimulation::divideLabor( ){
 
-  int* globalIndex;
-
   int nComponents;
   MoleculeStamp** compStamps;
   randomSPRNG *myRandom;
@@ -67,7 +65,7 @@ int* mpiSimulation::divideLabor( void ){
   nComponents = entryPlug->nComponents;
   compStamps = entryPlug->compStamps;
   componentsNmol = entryPlug->componentsNmol;
-  AtomsPerProc = new int[mpiPlug->numberProcessors];
+  AtomsPerProc = new int[mpiPlug->nProcessors];
   
   mpiPlug->nAtomsGlobal = entryPlug->n_atoms;
   mpiPlug->nBondsGlobal = entryPlug->n_bonds;
@@ -75,14 +73,14 @@ int* mpiSimulation::divideLabor( void ){
   mpiPlug->nTorsionsGlobal = entryPlug->n_torsions;
   mpiPlug->nSRIGlobal = entryPlug->n_SRI;
   mpiPlug->nMolGlobal = entryPlug->n_mol;
+  mpiPlug->nGroupsGlobal = entryPlug->ngroup;
 
-  
   myRandom = new randomSPRNG( baseSeed );
 
   a = 3.0 * (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
 
   // Initialize things that we'll send out later:
-  for (i = 0; i < mpiPlug->numberProcessors; i++ ) {
+  for (i = 0; i < mpiPlug->nProcessors; i++ ) {
     AtomsPerProc[i] = 0;
   }
   for (i = 0; i < mpiPlug->nMolGlobal; i++ ) {
@@ -97,7 +95,7 @@ int* mpiSimulation::divideLabor( void ){
     
   if (mpiPlug->myNode == 0) {
     numerator = (double) entryPlug->n_atoms;
-    denominator = (double) mpiPlug->numberProcessors;
+    denominator = (double) mpiPlug->nProcessors;
     precast = numerator / denominator;
     nTarget = (int)( precast + 0.5 );
 
@@ -122,7 +120,7 @@ int* mpiSimulation::divideLabor( void ){
         
         // Pick a processor at random
 
-        which_proc = (int) (myRandom->getRandom() * mpiPlug->numberProcessors);
+        which_proc = (int) (myRandom->getRandom() * mpiPlug->nProcessors);
 
         // How many atoms does this processor have?
         
@@ -206,7 +204,7 @@ int* mpiSimulation::divideLabor( void ){
     MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal, 
 	      MPI_INT, 0, MPI_COMM_WORLD);
 
-    MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
+    MPI_Bcast(AtomsPerProc, mpiPlug->nProcessors,
 	      MPI_INT, 0, MPI_COMM_WORLD);    
   } else {
 
@@ -221,7 +219,7 @@ int* mpiSimulation::divideLabor( void ){
     MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal, 
 	      MPI_INT, 0, MPI_COMM_WORLD);
     
-    MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
+    MPI_Bcast(AtomsPerProc, mpiPlug->nProcessors,
 	      MPI_INT, 0, MPI_COMM_WORLD);
 
 
@@ -271,31 +269,50 @@ int* mpiSimulation::divideLabor( void ){
 	   "Successfully divided the molecules among the processors.\n" );
   MPIcheckPoint();
 
-  mpiPlug->myNMol = nmol_local;
-  mpiPlug->myNlocal = natoms_local;
+  mpiPlug->nMolLocal = nmol_local;
+  mpiPlug->nAtomsLocal = natoms_local;
 
-  globalIndex = new int[mpiPlug->myNlocal];
+  globalAtomIndex.resize(mpiPlug->nAtomsLocal);
+  globalToLocalAtom.resize(mpiPlug->nAtomsGlobal);
   local_index = 0;
   for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
     if (AtomToProcMap[i] == mpiPlug->myNode) {
-      globalIndex[local_index] = i;
+      globalAtomIndex[local_index] = i;
+
+      globalToLocalAtom[i] = local_index;
       local_index++;
+      
     }
+    else
+       globalToLocalAtom[i] = -1;
   }
+
+  globalMolIndex.resize(mpiPlug->nMolLocal);
+  globalToLocalMol.resize(mpiPlug->nMolGlobal);
   
-  return globalIndex;
+  local_index = 0;
+  for (i = 0; i < mpiPlug->nMolGlobal; i++) {
+    if (MolToProcMap[i] == mpiPlug->myNode) {
+      globalMolIndex[local_index] = i;
+      globalToLocalMol[i] = local_index;
+      local_index++;
+    }
+    else
+      globalToLocalMol[i] = -1;
+  }
+  
 }
 
 
 void mpiSimulation::mpiRefresh( void ){
 
   int isError, i;
-  int *globalIndex = new int[mpiPlug->myNlocal];
+  int *globalIndex = new int[mpiPlug->nAtomsLocal];
 
   // Fortran indexing needs to be increased by 1 in order to get the 2 languages to
   // not barf
 
-  for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
+  for(i=0; i<mpiPlug->nAtomsLocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
 
   
   isError = 0;