--- trunk/OOPSE/libmdtools/mpiSimulation.cpp	2003/03/26 19:34:49	406
+++ trunk/OOPSE/libmdtools/mpiSimulation.cpp	2003/03/27 19:21:42	422
@@ -2,6 +2,7 @@
 
 #include <cstdlib>
 #include <cstring>
+#include <cmath>
 #include <mpi.h>
 #include <mpi++.h>
 
@@ -10,6 +11,7 @@
 #include "fortranWrappers.hpp"
 #include "randomSPRNG.hpp"
 
+#define BASE_SEED 123456789
 
 mpiSimulation* mpiSim;
 
@@ -23,7 +25,6 @@ mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
 
   MolToProcMap = new int[entryPlug->n_mol];
   MolComponentType = new int[entryPlug->n_mol];
-
   AtomToProcMap = new int[entryPlug->n_atoms];
 
   mpiSim = this;
@@ -33,6 +34,10 @@ mpiSimulation::~mpiSimulation(){
 
 mpiSimulation::~mpiSimulation(){
   
+  delete[] MolToProcMap;
+  delete[] MolComponentType;
+  delete[] AtomToProcMap;
+
   delete mpiPlug;
   // perhaps we should let fortran know the party is over.
   
@@ -44,7 +49,7 @@ int* mpiSimulation::divideLabor( void ){
 
   int nComponents;
   MoleculeStamp** compStamps;
-  randomSPRNG myRandom;
+  randomSPRNG *myRandom;
   int* componentsNmol;
   int* AtomsPerProc;
 
@@ -58,8 +63,11 @@ int* mpiSimulation::divideLabor( void ){
   int molIndex, atomIndex, compIndex, compStart;
   int done;
   int nLocal, molLocal;
-  int i, index;
+  int i, j, loops, which_proc, nmol_local, natoms_local;
+  int nmol_global, natoms_global;
+  int local_index, index;
   int smallDiff, bigDiff;
+  int baseSeed = BASE_SEED;
 
   int testSum;
 
@@ -75,7 +83,7 @@ int* mpiSimulation::divideLabor( void ){
   mpiPlug->nSRIGlobal = entryPlug->n_SRI;
   mpiPlug->nMolGlobal = entryPlug->n_mol;
 
-  myRandom = new randomSPRNG();
+  myRandom = new randomSPRNG( baseSeed );
 
   a = (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
 
@@ -120,7 +128,7 @@ int* mpiSimulation::divideLabor( void ){
         
         // Pick a processor at random
 
-        which_proc = (int) (myRandom.getRandom() * mpiPlug->numberProcessors);
+        which_proc = (int) (myRandom->getRandom() * mpiPlug->numberProcessors);
 
         // How many atoms does this processor have?
         
@@ -131,7 +139,7 @@ int* mpiSimulation::divideLabor( void ){
 
         if (old_atoms >= nTarget) continue;
 
-        add_atoms = compStamps[MolComponentType[i]]->getNatoms();
+        add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
         new_atoms = old_atoms + add_atoms;
     
         // If we can add this molecule to this processor without sending
@@ -141,8 +149,8 @@ int* mpiSimulation::divideLabor( void ){
           MolToProcMap[i] = which_proc;
           AtomsPerProc[which_proc] += add_atoms;
           for (j = 0 ; j < add_atoms; j++ ) {
-            atomIndex++;
-            AtomToProcMap[atomIndex] = which_proc;
+	    AtomToProcMap[atomIndex] = which_proc;
+	    atomIndex++;
           }
           done = 1;
           continue;
@@ -164,8 +172,8 @@ int* mpiSimulation::divideLabor( void ){
           MolToProcMap[i] = which_proc;
           AtomsPerProc[which_proc] += add_atoms;
           for (j = 0 ; j < add_atoms; j++ ) {
-            atomIndex++;
-            AtomToProcMap[atomIndex] = which_proc;
+	    AtomToProcMap[atomIndex] = which_proc;
+	    atomIndex++;
           }
           done = 1;
           continue;
@@ -180,15 +188,15 @@ int* mpiSimulation::divideLabor( void ){
         // where a = 1 / (average atoms per molecule)
 
         x = (double) (new_atoms - nTarget);
-        y = myRandom.getRandom();
+        y = myRandom->getRandom();
         
         if (exp(- a * x) > y) {
           MolToProcMap[i] = which_proc;
           AtomsPerProc[which_proc] += add_atoms;
           for (j = 0 ; j < add_atoms; j++ ) {
-            atomIndex++;
-            AtomToProcMap[atomIndex] = which_proc;
-          }
+	    AtomToProcMap[atomIndex] = which_proc;
+	    atomIndex++;
+           }
           done = 1;
           continue;
         } else {
@@ -200,31 +208,31 @@ int* mpiSimulation::divideLabor( void ){
 
     // Spray out this nonsense to all other processors:
 
-    MPI::COMM_WORLD.Bcast(&MolToProcMap, mpiPlug->nMolGlobal, 
+    MPI::COMM_WORLD.Bcast(MolToProcMap, mpiPlug->nMolGlobal, 
                           MPI_INT, 0);
 
-    MPI::COMM_WORLD.Bcast(&AtomToProcMap, mpiPlug->nAtomsGlobal, 
+    MPI::COMM_WORLD.Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal, 
                           MPI_INT, 0);
 
-    MPI::COMM_WORLD.Bcast(&MolComponentType, mpiPlug->nMolGlobal, 
+    MPI::COMM_WORLD.Bcast(MolComponentType, mpiPlug->nMolGlobal, 
                           MPI_INT, 0);
 
-    MPI::COMM_WORLD.Bcast(&AtomsPerProc, mpiPlug->numberProcessors,
+    MPI::COMM_WORLD.Bcast(AtomsPerProc, mpiPlug->numberProcessors,
                           MPI_INT, 0);    
   } else {
 
     // Listen to your marching orders from processor 0:
     
-    MPI::COMM_WORLD.Bcast(&MolToProcMap, mpiPlug->nMolGlobal, 
+    MPI::COMM_WORLD.Bcast(MolToProcMap, mpiPlug->nMolGlobal, 
                           MPI_INT, 0);
     
-    MPI::COMM_WORLD.Bcast(&AtomToProcMap, mpiPlug->nAtomsGlobal, 
+    MPI::COMM_WORLD.Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal, 
                           MPI_INT, 0);
 
-    MPI::COMM_WORLD.Bcast(&MolComponentType, mpiPlug->nMolGlobal, 
+    MPI::COMM_WORLD.Bcast(MolComponentType, mpiPlug->nMolGlobal, 
                           MPI_INT, 0);
     
-    MPI::COMM_WORLD.Bcast(&AtomsPerProc, mpiPlug->numberProcessors,
+    MPI::COMM_WORLD.Bcast(AtomsPerProc, mpiPlug->numberProcessors,
                           MPI_INT, 0);
   }
 
@@ -277,21 +285,12 @@ int* mpiSimulation::divideLabor( void ){
   local_index = 0;
   for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
     if (AtomToProcMap[i] == mpiPlug->myNode) {
-      local_index++;
       globalIndex[local_index] = i;
+      local_index++;
     }
   }
-  
-
-
-
-   index = mpiPlug->myAtomStart;
-//   for( i=0; i<mpiPlug->myNlocal; i++){
-//     globalIndex[i] = index;
-//     index++;
-//   }
-
-//   return globalIndex;
+ 
+  return globalIndex;
 }