--- trunk/mdtools/mpi_implementation/mpiSimulation.cpp	2003/01/28 22:16:55	252
+++ trunk/mdtools/mpi_implementation/mpiSimulation.cpp	2003/01/30 15:20:21	253
@@ -1,4 +1,4 @@
-i#include <cstdlib>
+#include <cstdlib>
 #include <cstring>
 #include <mpi.h>
 
@@ -19,7 +19,7 @@ mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
 mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
 {
   entryPlug = the_entryPlug;
-  mpiPlug = new MpiSimData;
+  mpiPlug = new mpiSimData;
   
   mpiPlug->numberProcessors = MPI::COMM_WORLD.Get_size();
   mpiPlug->myNode = worldRank;
@@ -44,8 +44,10 @@ void mpiSimulation::wrapMe(){
 
 
 
-void mpiSimulation::divideLabor( void ){
+int* mpiSimulation::divideLabor( void ){
 
+  int* globalIndex;
+
   int nComponents;
   MoleculeStamp** compStamps;
   int* componentsNmol;
@@ -58,7 +60,7 @@ void mpiSimulation::divideLabor( void ){
   int molIndex, atomIndex, compIndex, compStart;
   int done;
   int nLocal, molLocal;
-  int i;
+  int i, index;
   int smallDiff, bigDiff;
 
   int testSum;
@@ -72,7 +74,7 @@ void mpiSimulation::divideLabor( void ){
   mpiPlug->nBendsGlobal = entryPlug->n_bends;
   mpiPlug->nTorsionsGlobal = entryPlug->n_torsions;
   mpiPlug->nSRIGlobal = entryPlug->n_SRI;
-  mpiPlug->nMolGlobal = entryPlug->n_nmol;
+  mpiPlug->nMolGlobal = entryPlug->n_mol;
 
   numerator = (double) entryPlug->n_atoms;
   denominator = (double) mpiPlug->numberProcessors;
@@ -183,6 +185,15 @@ void mpiSimulation::divideLabor( void ){
   MPIcheckPoint();
 
   // lets create the identity array
+
+  globalIndex = new int[mpiPlug->myNlocal];
+  index = mpiPlug->myAtomStart;
+  for( i=0; i<mpiPlug->myNlocal; i++){
+    globalIndex[i] = index;
+    index++;
+  }
+
+  return globalIndex;
 }
 
 
@@ -190,3 +201,30 @@ void wrapSimParallel(void (*fSub)(mpiSimData*, int*, i
   
   mpiSim->setInternal( fSub );
 }
+
+
+void mpiSimulation::mpiRefresh( void ){
+
+  int isError, i;
+  int *globalIndex = new int[mpiPlug->myNlocal];
+
+  for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex();
+
+  
+  isError = 0;
+  setFsimParallel( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError );
+  if( isError ){
+
+    sprintf( painCave.errMsg,
+	     "mpiRefresh errror: fortran didn't like something we gave it.\n" );
+    painCave.isFatal = 1;
+    simError();
+  }
+
+  delete[] globalIndex;
+
+  sprintf( checkPointMsg,
+	   " mpiRefresh successful.\n" );
+  MPIcheckPoint();
+}
+