--- trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/10/28 16:03:37	829
+++ trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/10/29 00:19:10	837
@@ -28,13 +28,13 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
 #ifdef IS_MPI
   if(worldRank == 0 ){
 #endif // is_mpi
-    
+
     strcpy( outName, entry_plug->sampleName );
-    
+
     outFile.open(outName, ios::out | ios::trunc );
-    
+
     if( !outFile ){
-      
+
       sprintf( painCave.errMsg,
 	       "Could not open \"%s\" for dump output.\n",
 	       outName);
@@ -67,7 +67,7 @@ void DumpWriter::writeDump( double currentTime ){
 }
 
 void DumpWriter::writeDump( double currentTime ){
-  
+
   const int BUFFERSIZE = 2000;
   char tempBuffer[BUFFERSIZE];
   char writeLine[BUFFERSIZE];
@@ -83,17 +83,17 @@ void DumpWriter::writeDump( double currentTime ){
   DirectionalAtom* dAtom;
   Atom** atoms = entry_plug->atoms;
   double pos[3], vel[3];
-    
-  
+
+
   // write current frame to the eor file
 
   this->writeFinal( currentTime );
 
 #ifndef IS_MPI
-    
+
   outFile << nAtoms << "\n";
-    
-  outFile << currentTime << ";\t" 
+
+  outFile << currentTime << ";\t"
 	  << entry_plug->Hmat[0][0] << "\t"
 	  << entry_plug->Hmat[1][0] << "\t"
 	  << entry_plug->Hmat[2][0] << ";\t"
@@ -104,10 +104,13 @@ void DumpWriter::writeDump( double currentTime ){
 
 	  << entry_plug->Hmat[0][2] << "\t"
 	  << entry_plug->Hmat[1][2] << "\t"
-	  << entry_plug->Hmat[2][2] << ";\n";
-    
+	  << entry_plug->Hmat[2][2] << ";";
+  //write out additional parameters, such as chi and eta
+  outFile << entry_plug->the_integrator->getAdditionalParameters();
+  outFile << endl;
+
   for( i=0; i<nAtoms; i++ ){
-      
+
     atoms[i]->getPos(pos);
     atoms[i]->getVel(vel);
 
@@ -123,10 +126,10 @@ void DumpWriter::writeDump( double currentTime ){
     strcpy( writeLine, tempBuffer );
 
     if( atoms[i]->isDirectional() ){
-	
+
       dAtom = (DirectionalAtom *)atoms[i];
       dAtom->getQ( q );
-	
+
       sprintf( tempBuffer,
 	       "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
 	       q[0],
@@ -140,7 +143,7 @@ void DumpWriter::writeDump( double currentTime ){
     }
     else
       strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
-      
+
     outFile << writeLine;
   }
   outFile.flush();
@@ -155,42 +158,44 @@ void DumpWriter::writeDump( double currentTime ){
 
   MPI_Status istatus;
   int *AtomToProcMap = mpiSim->getAtomToProcMap();
-  
+
   // write out header and node 0's coordinates
-  
+
   if( worldRank == 0 ){
     outFile << mpiSim->getTotAtoms() << "\n";
-  
-    outFile << currentTime << ";\t" 
+
+    outFile << currentTime << ";\t"
 	    << entry_plug->Hmat[0][0] << "\t"
 	    << entry_plug->Hmat[1][0] << "\t"
 	    << entry_plug->Hmat[2][0] << ";\t"
-      
+
 	    << entry_plug->Hmat[0][1] << "\t"
 	    << entry_plug->Hmat[1][1] << "\t"
 	    << entry_plug->Hmat[2][1] << ";\t"
-      
+
 	    << entry_plug->Hmat[0][2] << "\t"
 	    << entry_plug->Hmat[1][2] << "\t"
-	    << entry_plug->Hmat[2][2] << ";\n";
-    
+	    << entry_plug->Hmat[2][2] << ";";
+
+    outFile << entry_plug->the_integrator->getAdditionalParameters();
+    outFile << endl;
     outFile.flush();
     for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
       // Get the Node number which has this atom;
-      
-      which_node = AtomToProcMap[i];     
-      
+
+      which_node = AtomToProcMap[i];
+
       if (which_node == 0 ) {
-	
+
 	haveError = 0;
 	which_atom = i;
-	local_index=-1;        
+	local_index=-1;
         for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
           if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
         }
         if (local_index != -1) {
           //format the line
-	  
+
 	  atoms[local_index]->getPos(pos);
 	  atoms[local_index]->getVel(vel);
 
@@ -204,12 +209,12 @@ void DumpWriter::writeDump( double currentTime ){
 		   vel[1],
 		   vel[2]); // check here.
           strcpy( writeLine, tempBuffer );
-	  
+
           if( atoms[local_index]->isDirectional() ){
-            
+
             dAtom = (DirectionalAtom *)atoms[local_index];
             dAtom->getQ( q );
-            
+
             sprintf( tempBuffer,
                      "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
                      q[0],
@@ -220,10 +225,10 @@ void DumpWriter::writeDump( double currentTime ){
                      dAtom->getJy(),
                      dAtom->getJz());
             strcat( writeLine, tempBuffer );
-	    
+
 	  }
 	  else
-	    strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );       
+	    strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
 	}
 	else {
 	  sprintf(painCave.errMsg,
@@ -231,54 +236,54 @@ void DumpWriter::writeDump( double currentTime ){
 		  i, worldRank );
 	  haveError= 1;
 	  simError();
-	} 
-	
+	}
+
 	if(haveError) nodeZeroError();
 
       }
       else {
 	myStatus = 1;
-	MPI_Send(&myStatus, 1, MPI_INT, which_node, 
+	MPI_Send(&myStatus, 1, MPI_INT, which_node,
 		 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
-        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, 
+        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
 		 MPI_COMM_WORLD);
         MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
 		 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
-        MPI_Recv(&myStatus, 1, MPI_INT, which_node, 
+        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
 		 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
-	
+
 	if(!myStatus) nodeZeroError();
 
       }
-      
+
       outFile << writeLine;
       outFile.flush();
     }
-    
+
     // kill everyone off:
     myStatus = -1;
-    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
-      MPI_Send(&myStatus, 1, MPI_INT, j, 
+    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
+      MPI_Send(&myStatus, 1, MPI_INT, j,
 	       TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
     }
 
   } else {
-    
+
     done = 0;
     while (!done) {
-      
-      MPI_Recv(&myStatus, 1, MPI_INT, 0, 
+
+      MPI_Recv(&myStatus, 1, MPI_INT, 0,
 	       TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
 
       if(!myStatus) anonymousNodeDie();
-      
+
       if(myStatus < 0) break;
 
-      MPI_Recv(&which_atom, 1, MPI_INT, 0, 
+      MPI_Recv(&which_atom, 1, MPI_INT, 0,
 	       TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
-      
+
       myStatus = 1;
-      local_index=-1;        
+      local_index=-1;
       for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
 	if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
       }
@@ -298,12 +303,12 @@ void DumpWriter::writeDump( double currentTime ){
 		 vel[1],
 		 vel[2]); // check here.
 	strcpy( writeLine, tempBuffer );
-	
+
 	if( atoms[local_index]->isDirectional() ){
-	  
+
 	  dAtom = (DirectionalAtom *)atoms[local_index];
 	  dAtom->getQ( q );
-	  
+
 	  sprintf( tempBuffer,
 		   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
 		   q[0],
@@ -318,7 +323,7 @@ void DumpWriter::writeDump( double currentTime ){
 	else{
 	  strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
 	}
-      } 
+      }
       else {
 	sprintf(painCave.errMsg,
 		"Atom %d not found on processor %d\n",
@@ -329,12 +334,12 @@ void DumpWriter::writeDump( double currentTime ){
 	strcpy( writeLine, "Hello, I'm an error.\n");
       }
 
-      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, 
+      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
 	       TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
-      MPI_Send( &myStatus, 1, MPI_INT, 0, 
+      MPI_Send( &myStatus, 1, MPI_INT, 0,
 		TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
     }
-  }  
+  }
   outFile.flush();
   sprintf( checkPointMsg,
 	   "Sucessfully took a dump.\n");
@@ -353,7 +358,7 @@ void DumpWriter::writeFinal(double finalTime){
 
   const int BUFFERSIZE = 2000;
   char tempBuffer[BUFFERSIZE];
-  char writeLine[BUFFERSIZE];  
+  char writeLine[BUFFERSIZE];
 
   double q[4];
   DirectionalAtom* dAtom;
@@ -364,15 +369,15 @@ void DumpWriter::writeFinal(double finalTime){
 #else //is_mpi
   int nAtoms = entry_plug->n_atoms;
 #endif //is_mpi
-  
+
   double pos[3], vel[3];
-  
+
 #ifdef IS_MPI
   if(worldRank == 0 ){
 #endif // is_mpi
-    
+
     strcpy( finalName, entry_plug->finalName );
-    
+
     finalOut.open( finalName, ios::out | ios::trunc );
     if( !finalOut ){
       sprintf( painCave.errMsg,
@@ -381,40 +386,44 @@ void DumpWriter::writeFinal(double finalTime){
       painCave.isFatal = 1;
       simError();
     }
-    
+
     // finalOut.setf( ios::scientific );
-    
+
 #ifdef IS_MPI
   }
-  
+
   sprintf(checkPointMsg,"Opened file for final configuration\n");
-  MPIcheckPoint();  
-  
+  MPIcheckPoint();
+
 #endif //is_mpi
 
-  
+
 #ifndef IS_MPI
-    
+
   finalOut << nAtoms << "\n";
-    
+
   finalOut << finalTime << ";\t"
 	   << entry_plug->Hmat[0][0] << "\t"
 	   << entry_plug->Hmat[1][0] << "\t"
 	   << entry_plug->Hmat[2][0] << ";\t"
-    
+
 	   << entry_plug->Hmat[0][1] << "\t"
 	   << entry_plug->Hmat[1][1] << "\t"
 	   << entry_plug->Hmat[2][1] << ";\t"
-    
+
 	   << entry_plug->Hmat[0][2] << "\t"
 	   << entry_plug->Hmat[1][2] << "\t"
-	   << entry_plug->Hmat[2][2] << ";\n";
-  
+	   << entry_plug->Hmat[2][2] << ";";
+
+  //write out additional parameters, such as chi and eta
+  finalOut << entry_plug->the_integrator->getAdditionalParameters();
+  finalOut << endl;
+
   for( i=0; i<nAtoms; i++ ){
-      
+
     atoms[i]->getPos(pos);
     atoms[i]->getVel(vel);
-    
+
     sprintf( tempBuffer,
 	     "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
 	     atoms[i]->getType(),
@@ -427,10 +436,10 @@ void DumpWriter::writeFinal(double finalTime){
     strcpy( writeLine, tempBuffer );
 
     if( atoms[i]->isDirectional() ){
-	
+
       dAtom = (DirectionalAtom *)atoms[i];
       dAtom->getQ( q );
-	
+
       sprintf( tempBuffer,
 	       "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
 	       q[0],
@@ -444,14 +453,14 @@ void DumpWriter::writeFinal(double finalTime){
     }
     else
       strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
-      
+
     finalOut << writeLine;
   }
   finalOut.flush();
   finalOut.close();
 
 #else // is_mpi
-  
+
   // first thing first, suspend fatalities.
   painCave.isEventLoop = 1;
 
@@ -462,41 +471,45 @@ void DumpWriter::writeFinal(double finalTime){
   int *AtomToProcMap = mpiSim->getAtomToProcMap();
 
   // write out header and node 0's coordinates
-  
+
   haveError = 0;
   if( worldRank == 0 ){
     finalOut << mpiSim->getTotAtoms() << "\n";
-    
+
     finalOut << finalTime << ";\t"
 	     << entry_plug->Hmat[0][0] << "\t"
 	     << entry_plug->Hmat[1][0] << "\t"
 	     << entry_plug->Hmat[2][0] << ";\t"
-      
+
 	     << entry_plug->Hmat[0][1] << "\t"
 	     << entry_plug->Hmat[1][1] << "\t"
 	     << entry_plug->Hmat[2][1] << ";\t"
-      
+
 	     << entry_plug->Hmat[0][2] << "\t"
 	     << entry_plug->Hmat[1][2] << "\t"
-	     << entry_plug->Hmat[2][2] << ";\n";
-    
+	     << entry_plug->Hmat[2][2] << ";";
+
+    //write out additional parameters, such as chi and eta
+    finalOut << entry_plug->the_integrator->getAdditionalParameters();
+    finalOut << endl;
+
     for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
       // Get the Node number which has this molecule:
-      
-      which_node = AtomToProcMap[i];     
-      
+
+      which_node = AtomToProcMap[i];
+
       if (which_node == mpiSim->getMyNode()) {
 
 	which_atom = i;
-	local_index=-1;        
+	local_index=-1;
         for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
           if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
         }
-        if (local_index != -1) {    
+        if (local_index != -1) {
 
 	  atoms[local_index]->getPos(pos);
 	  atoms[local_index]->getVel(vel);
-	  
+
 	  sprintf( tempBuffer,
 		   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
 		   atoms[local_index]->getType(),
@@ -507,12 +520,12 @@ void DumpWriter::writeFinal(double finalTime){
 		   vel[1],
 		   vel[2]);
 	  strcpy( writeLine, tempBuffer );
-	  
+
 	  if( atoms[local_index]->isDirectional() ){
-	    
+
 	    dAtom = (DirectionalAtom *)atoms[local_index];
 	    dAtom->getQ( q );
-	    
+
 	    sprintf( tempBuffer,
 		     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
 		     q[0],
@@ -525,7 +538,7 @@ void DumpWriter::writeFinal(double finalTime){
 	    strcat( writeLine, tempBuffer );
 	  }
 	  else
-	    strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );       
+	    strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
    	}
 	else {
 	  sprintf(painCave.errMsg,
@@ -533,53 +546,53 @@ void DumpWriter::writeFinal(double finalTime){
 		  i, worldRank );
 	  haveError= 1;
 	  simError();
-	} 
+	}
 
 	if(haveError) nodeZeroError();
-     
-      } 
+
+      }
       else {
-        
+
 	myStatus = 1;
-	MPI_Send(&myStatus, 1, MPI_INT, which_node, 
+	MPI_Send(&myStatus, 1, MPI_INT, which_node,
 		 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
         MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
 		 MPI_COMM_WORLD);
         MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
 		 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
-        MPI_Recv(&myStatus, 1, MPI_INT, which_node, 
+        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
 		 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
-	
+
 	if(!myStatus) nodeZeroError();
       }
-      
+
       finalOut << writeLine;
     }
-    
+
     // kill everyone off:
     myStatus = -1;
-    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
-      MPI_Send(&myStatus, 1, MPI_INT, j, 
+    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
+      MPI_Send(&myStatus, 1, MPI_INT, j,
 	       TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
     }
 
   } else {
-    
+
     done = 0;
     while (!done) {
 
-      MPI_Recv(&myStatus, 1, MPI_INT, 0, 
+      MPI_Recv(&myStatus, 1, MPI_INT, 0,
 	       TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
-      
+
       if(!myStatus) anonymousNodeDie();
-      
+
       if(myStatus < 0) break;
-      
-      MPI_Recv(&which_atom, 1, MPI_INT, 0, 
+
+      MPI_Recv(&which_atom, 1, MPI_INT, 0,
 	       TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
-      
+
       myStatus = 1;
-      local_index=-1;        
+      local_index=-1;
       for (j=0; j < mpiSim->getMyNlocal(); j++) {
 	if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
       }
@@ -599,12 +612,12 @@ void DumpWriter::writeFinal(double finalTime){
 		 vel[1],
 		 vel[2]); // check here.
 	strcpy( writeLine, tempBuffer );
-	
+
 	if( atoms[local_index]->isDirectional() ){
-	  
+
 	  dAtom = (DirectionalAtom *)atoms[local_index];
 	  dAtom->getQ( q );
-	  
+
 	  sprintf( tempBuffer,
 		   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
 		   q[0],
@@ -619,20 +632,20 @@ void DumpWriter::writeFinal(double finalTime){
 	else{
 	  strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
 	}
-      } 
+      }
       else {
 	sprintf(painCave.errMsg,
 		"Atom %d not found on processor %d\n",
 		which_atom, worldRank );
 	myStatus = 0;
 	simError();
-	
+
 	strcpy( writeLine, "Hello, I'm an error.\n");
       }
 
-      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, 
+      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
 	       TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
-      MPI_Send( &myStatus, 1, MPI_INT, 0, 
+      MPI_Send( &myStatus, 1, MPI_INT, 0,
 		TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
     }
   }
@@ -640,8 +653,8 @@ void DumpWriter::writeFinal(double finalTime){
   sprintf( checkPointMsg,
 	   "Sucessfully took a dump.\n");
   MPIcheckPoint();
-  
-  if( worldRank == 0 ) finalOut.close();    
+
+  if( worldRank == 0 ) finalOut.close();
 #endif // is_mpi
 }
 
@@ -653,17 +666,17 @@ void dWrite::nodeZeroError( void ){
 
 void dWrite::nodeZeroError( void ){
   int j, myStatus;
-  
+
   myStatus = 0;
-  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
-    MPI_Send( &myStatus, 1, MPI_INT, j, 
+  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
+    MPI_Send( &myStatus, 1, MPI_INT, j,
 	      TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
-  }  
-  
+  }
 
+
   MPI_Finalize();
   exit (0);
-  
+
 }
 
 void dWrite::anonymousNodeDie( void ){