--- trunk/mdtools/mpi_implementation/mpiSimulation.cpp	2002/12/05 18:53:40	195
+++ trunk/mdtools/mpi_implementation/mpiSimulation.cpp	2003/01/30 15:20:21	253
@@ -1,33 +1,57 @@
-i#include <cstdlib>
+#include <cstdlib>
 #include <cstring>
 #include <mpi.h>
 
 #include "mpiSimulation.hpp"
 #include "simError.h"
 
+extern "C"{
+  void wrapsimparallelmod_( void (*wrapFunction)(void (*fSub)( mpiSimData*,
+							       int*, int*, 
+							       int*)));
+}
 
+void wrapSimParallel(void (*fSub)(mpiSimData*, int*, int*, int*));
 
+
+mpiSimulation* mpiSim;
+
 mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
 {
   entryPlug = the_entryPlug;
+  mpiPlug = new mpiSimData;
   
-  numberProcessors = MPI::COMM_WORLD.Get_size();
-  myNode = worldRank;
+  mpiPlug->numberProcessors = MPI::COMM_WORLD.Get_size();
+  mpiPlug->myNode = worldRank;
   
-  // let the simulation know were there.
-  entryPlug->mpiSim = this;
+  mpiSim = this;
+  wrapMe();
+
 }
 
 
 mpiSimulation::~mpiSimulation(){
   
-  // empty for now
+  delete mpiPlug;
+  // perhaps we should let fortran know the party is over.
   
 }
 
+void mpiSimulation::wrapMe(){
 
-void mpiSimulation::divideLabor(int nComponents, MoleculeStamp** compStamps, int* componentsNmol ){
-  
+  wrapsimparallelmod_( wrapSimParallel );
+}
+
+
+
+int* mpiSimulation::divideLabor( void ){
+
+  int* globalIndex;
+
+  int nComponents;
+  MoleculeStamp** compStamps;
+  int* componentsNmol;
+
   double numerator;
   double denominator;
   double precast;
@@ -35,14 +59,25 @@ void mpiSimulation::divideLabor(int nComponents, Molec
   int nTarget;
   int molIndex, atomIndex, compIndex, compStart;
   int done;
-  int nLocal;
-  int i;
+  int nLocal, molLocal;
+  int i, index;
   int smallDiff, bigDiff;
 
   int testSum;
 
+  nComponents = entryPlug->nComponents;
+  compStamps = entryPlug->compStamps;
+  componentsNmol = entryPlug->componentsNmol;
+
+  mpiPlug->nAtomsGlobal = entryPlug->n_atoms;
+  mpiPlug->nBondsGlobal = entryPlug->n_bonds;
+  mpiPlug->nBendsGlobal = entryPlug->n_bends;
+  mpiPlug->nTorsionsGlobal = entryPlug->n_torsions;
+  mpiPlug->nSRIGlobal = entryPlug->n_SRI;
+  mpiPlug->nMolGlobal = entryPlug->n_mol;
+
   numerator = (double) entryPlug->n_atoms;
-  denominator = (double) numberProcessors;
+  denominator = (double) mpiPlug->numberProcessors;
   precast = numerator / denominator;
   nTarget = (int)( precast + 0.5 );
   
@@ -50,14 +85,15 @@ void mpiSimulation::divideLabor(int nComponents, Molec
   atomIndex = 0;
   compIndex = 0;
   compStart = 0;
-  for( i=0; i<(numberProcessors-1); i++){
+  for( i=0; i<(mpiPlug->numberProcessors-1); i++){
     
     done = 0;
     nLocal = 0;
+    molLocal = 0;
 
-    if( i == myNode ){
-      myMolStart = molIndex;
-      myAtomStart = atomIndex;
+    if( i == mpiPlug->myNode ){
+      mpiPlug->myMolStart = molIndex;
+      mpiPlug->myAtomStart = atomIndex;
     }
     
     while( !done ){
@@ -71,6 +107,7 @@ void mpiSimulation::divideLabor(int nComponents, Molec
       nLocal += compStamps[compIndex]->getNAtoms();
       atomIndex += compStamps[compIndex]->getNAtoms();
       molIndex++;
+      molLocal++;
       
       if ( nLocal == nTarget ) done = 1;
       
@@ -83,6 +120,7 @@ void mpiSimulation::divideLabor(int nComponents, Molec
 	if( bigDiff < smallDiff ) done = 1;
 	else{
 	  molIndex--;
+	  molLocal--;
 	  atomIndex -= compStamps[compIndex]->getNAtoms();
 	  nLocal -= compStamps[compIndex]->getNAtoms();
 	  done = 1;
@@ -90,23 +128,25 @@ void mpiSimulation::divideLabor(int nComponents, Molec
       }
     }
     
-    if( i == myNode ){
-      myMolEnd = (molIndex - 1);
-      myAtomEnd = (atomIndex - 1);
-      myNlocal = nLocal;
+    if( i == mpiPlug->myNode ){
+      mpiPlug->myMolEnd = (molIndex - 1);
+      mpiPlug->myAtomEnd = (atomIndex - 1);
+      mpiPlug->myNlocal = nLocal;
+      mpiPlug->myMol = molLocal;
     }
     
     numerator = (double)( entryPlug->n_atoms - atomIndex );
-    denominator = (double)( numberProcessors - (i+1) );
+    denominator = (double)( mpiPlug->numberProcessors - (i+1) );
     precast = numerator / denominator;
     nTarget = (int)( precast + 0.5 );
   }
   
-  if( myNode == numberProcessors-1 ){
-      myMolStart = molIndex;
-      myAtomStart = atomIndex;
+  if( mpiPlug->myNode == mpiPlug->numberProcessors-1 ){
+      mpiPlug->myMolStart = molIndex;
+      mpiPlug->myAtomStart = atomIndex;
 
       nLocal = 0;
+      molLocal = 0;
       while( compIndex < nComponents ){
 	
 	if( (molIndex-compStart) >= componentsNmol[compIndex] ){
@@ -118,17 +158,19 @@ void mpiSimulation::divideLabor(int nComponents, Molec
 	nLocal += compStamps[compIndex]->getNAtoms();
 	atomIndex += compStamps[compIndex]->getNAtoms();
 	molIndex++;
+	molLocal++;
       }
       
-      myMolEnd = (molIndex - 1);
-      myAtomEnd = (atomIndex - 1);
-      myNlocal = nLocal;   
+      mpiPlug->myMolEnd = (molIndex - 1);
+      mpiPlug->myAtomEnd = (atomIndex - 1);
+      mpiPlug->myNlocal = nLocal;  
+      mpiPlug->myMol = molLocal;
   }
 
 
-  MPI_Allreduce( &Nlocal, &testSum, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD );
+  MPI_Allreduce( &nLocal, &testSum, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD );
   
-  if( myNode == 0 ){
+  if( mpiPlug->myNode == 0 ){
     if( testSum != entryPlug->n_atoms ){
       sprintf( painCave.errMsg,
 	       "The summ of all nLocals, %d, did not equal the total number of atoms, %d.\n",
@@ -141,4 +183,48 @@ void mpiSimulation::divideLabor(int nComponents, Molec
   sprintf( checkPointMsg,
 	   "Successfully divided the molecules among the processors.\n" );
   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;
 }
+
+
+void wrapSimParallel(void (*fSub)(mpiSimData*, int*, int*, int*)){
+  
+  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();
+}
+