--- trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/04/01 16:49:17	440
+++ trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/10/28 16:03:37	829
@@ -1,10 +1,11 @@
-#include <cstring>
+#define _FILE_OFFSET_BITS 64
+
+#include <string.h>
 #include <iostream>
 #include <fstream>
 
 #ifdef IS_MPI
 #include <mpi.h>
-#include <mpi++.h>
 #include "mpiSimulation.hpp"
 #define TAKE_THIS_TAG_CHAR 1
 #define TAKE_THIS_TAG_INT 2
@@ -28,8 +29,6 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
   if(worldRank == 0 ){
 #endif // is_mpi
     
- 
-    
     strcpy( outName, entry_plug->sampleName );
     
     outFile.open(outName, ios::out | ios::trunc );
@@ -42,7 +41,7 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
       painCave.isFatal = 1;
       simError();
     }
-  
+
     //outFile.setf( ios::scientific );
 
 #ifdef IS_MPI
@@ -73,34 +72,54 @@ void DumpWriter::writeDump( double currentTime ){
   char tempBuffer[BUFFERSIZE];
   char writeLine[BUFFERSIZE];
 
-  int i, j, which_node, done, game_over, which_atom, local_index;
+  int i;
+#ifdef IS_MPI
+  int j, which_node, done, which_atom, local_index;
+#else //is_mpi
+  int nAtoms = entry_plug->n_atoms;
+#endif //is_mpi
+
   double q[4];
   DirectionalAtom* dAtom;
-  int nAtoms = entry_plug->n_atoms;
   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" 
-	  << entry_plug->box_x << "\t"
-	  << entry_plug->box_y << "\t"
-	  << entry_plug->box_z << "\n";
+  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";
     
   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(),
-	     atoms[i]->getX(),
-	     atoms[i]->getY(),
-	     atoms[i]->getZ(),
-	     atoms[i]->get_vx(),
-	     atoms[i]->get_vy(),
-	     atoms[i]->get_vz());
+	     pos[0],
+	     pos[1],
+	     pos[2],
+	     vel[0],
+	     vel[1],
+	     vel[2]);
     strcpy( writeLine, tempBuffer );
 
     if( atoms[i]->isDirectional() ){
@@ -134,18 +153,27 @@ void DumpWriter::writeDump( double currentTime ){
   int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
   int haveError;
 
-  MPI::Status istatus;
+  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" 
+	    << 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";
     
-    outFile << currentTime << "\t" 
-	    << entry_plug->box_x << "\t"
-	    << entry_plug->box_y << "\t"
-	    << entry_plug->box_z << "\n";
     outFile.flush();
     for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
       // Get the Node number which has this atom;
@@ -162,15 +190,19 @@ void DumpWriter::writeDump( double currentTime ){
         }
         if (local_index != -1) {
           //format the line
+	  
+	  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(),
-                   atoms[local_index]->getX(),
-                   atoms[local_index]->getY(),
-                   atoms[local_index]->getZ(),
-                   atoms[local_index]->get_vx(),
-                   atoms[local_index]->get_vy(),
-                   atoms[local_index]->get_vz()); // check here.
+		   pos[0],
+		   pos[1],
+		   pos[2],
+		   vel[0],
+		   vel[1],
+		   vel[2]); // check here.
           strcpy( writeLine, tempBuffer );
 	  
           if( atoms[local_index]->isDirectional() ){
@@ -206,13 +238,14 @@ void DumpWriter::writeDump( double currentTime ){
       }
       else {
 	myStatus = 1;
-	MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, 
-                             TAKE_THIS_TAG_INT);
-        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
-        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
-			     TAKE_THIS_TAG_CHAR, istatus);
-        MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, 
-			     TAKE_THIS_TAG_INT, istatus);
+	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, 
+		 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
 	
 	if(!myStatus) nodeZeroError();
 
@@ -225,8 +258,8 @@ void DumpWriter::writeDump( double currentTime ){
     // kill everyone off:
     myStatus = -1;
     for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
-      MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, j, 
-			   TAKE_THIS_TAG_INT);
+      MPI_Send(&myStatus, 1, MPI_INT, j, 
+	       TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
     }
 
   } else {
@@ -234,15 +267,15 @@ void DumpWriter::writeDump( double currentTime ){
     done = 0;
     while (!done) {
       
-      MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, 
-                           TAKE_THIS_TAG_INT, istatus);
+      MPI_Recv(&myStatus, 1, MPI_INT, 0, 
+	       TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
 
       if(!myStatus) anonymousNodeDie();
       
       if(myStatus < 0) break;
 
-      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, 
-                           TAKE_THIS_TAG_INT, istatus);
+      MPI_Recv(&which_atom, 1, MPI_INT, 0, 
+	       TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
       
       myStatus = 1;
       local_index=-1;        
@@ -251,15 +284,19 @@ void DumpWriter::writeDump( double currentTime ){
       }
       if (local_index != -1) {
 	//format the line
+
+	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(),
-		 atoms[local_index]->getX(),
-		 atoms[local_index]->getY(),
-		 atoms[local_index]->getZ(),
-		 atoms[local_index]->get_vx(),
-		 atoms[local_index]->get_vy(),
-		 atoms[local_index]->get_vz()); // check here.
+		 pos[0],
+		 pos[1],
+		 pos[2],
+		 vel[0],
+		 vel[1],
+		 vel[2]); // check here.
 	strcpy( writeLine, tempBuffer );
 	
 	if( atoms[local_index]->isDirectional() ){
@@ -292,10 +329,10 @@ void DumpWriter::writeDump( double currentTime ){
 	strcpy( writeLine, "Hello, I'm an error.\n");
       }
 
-      MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, 
-			   TAKE_THIS_TAG_CHAR);
-      MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, 
-			    TAKE_THIS_TAG_INT);
+      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, 
+	       TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
+      MPI_Send( &myStatus, 1, MPI_INT, 0, 
+		TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
     }
   }  
   outFile.flush();
@@ -309,7 +346,7 @@ void DumpWriter::writeDump( double currentTime ){
 #endif // is_mpi
 }
 
-void DumpWriter::writeFinal(){
+void DumpWriter::writeFinal(double finalTime){
 
   char finalName[500];
   ofstream finalOut;
@@ -320,10 +357,15 @@ void DumpWriter::writeFinal(){
 
   double q[4];
   DirectionalAtom* dAtom;
-  int nAtoms = entry_plug->n_atoms;
   Atom** atoms = entry_plug->atoms;
-  int i, j, which_node, done, game_over, which_atom, local_index;
+  int i;
+#ifdef IS_MPI
+  int j, which_node, done, which_atom, local_index;
+#else //is_mpi
+  int nAtoms = entry_plug->n_atoms;
+#endif //is_mpi
   
+  double pos[3], vel[3];
   
 #ifdef IS_MPI
   if(worldRank == 0 ){
@@ -355,21 +397,33 @@ void DumpWriter::writeFinal(){
     
   finalOut << nAtoms << "\n";
     
-  finalOut << entry_plug->box_x << "\t"
-	   << entry_plug->box_y << "\t"
-	   << entry_plug->box_z << "\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";
   
   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(),
-	     atoms[i]->getX(),
-	     atoms[i]->getY(),
-	     atoms[i]->getZ(),
-	     atoms[i]->get_vx(),
-	     atoms[i]->get_vy(),
-	     atoms[i]->get_vz());
+	     pos[0],
+	     pos[1],
+	     pos[2],
+	     vel[0],
+	     vel[1],
+	     vel[2]);
     strcpy( writeLine, tempBuffer );
 
     if( atoms[i]->isDirectional() ){
@@ -404,7 +458,7 @@ void DumpWriter::writeFinal(){
   int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
   int haveError;
 
-  MPI::Status istatus;
+  MPI_Status istatus;
   int *AtomToProcMap = mpiSim->getAtomToProcMap();
 
   // write out header and node 0's coordinates
@@ -413,9 +467,18 @@ void DumpWriter::writeFinal(){
   if( worldRank == 0 ){
     finalOut << mpiSim->getTotAtoms() << "\n";
     
-    finalOut << entry_plug->box_x << "\t"
-	    << entry_plug->box_y << "\t"
-	    << entry_plug->box_z << "\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";
     
     for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
       // Get the Node number which has this molecule:
@@ -429,16 +492,20 @@ void DumpWriter::writeFinal(){
         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(),
-		   atoms[local_index]->getX(),
-		   atoms[local_index]->getY(),
-		   atoms[local_index]->getZ(),
-		   atoms[local_index]->get_vx(),
-		   atoms[local_index]->get_vy(),
-		   atoms[local_index]->get_vz());
+		   pos[0],
+		   pos[1],
+		   pos[2],
+		   vel[0],
+		   vel[1],
+		   vel[2]);
 	  strcpy( writeLine, tempBuffer );
 	  
 	  if( atoms[local_index]->isDirectional() ){
@@ -474,13 +541,14 @@ void DumpWriter::writeFinal(){
       else {
         
 	myStatus = 1;
-	MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, 
-                             TAKE_THIS_TAG_INT);
-        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
-        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
-			     TAKE_THIS_TAG_CHAR, istatus);
-        MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, 
-			     TAKE_THIS_TAG_INT, istatus);
+	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, 
+		 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
 	
 	if(!myStatus) nodeZeroError();
       }
@@ -491,8 +559,8 @@ void DumpWriter::writeFinal(){
     // kill everyone off:
     myStatus = -1;
     for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
-      MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, j, 
-			   TAKE_THIS_TAG_INT);
+      MPI_Send(&myStatus, 1, MPI_INT, j, 
+	       TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
     }
 
   } else {
@@ -500,15 +568,15 @@ void DumpWriter::writeFinal(){
     done = 0;
     while (!done) {
 
-      MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, 
-                           TAKE_THIS_TAG_INT, istatus);
+      MPI_Recv(&myStatus, 1, MPI_INT, 0, 
+	       TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
       
       if(!myStatus) anonymousNodeDie();
       
       if(myStatus < 0) break;
       
-      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, 
-                           TAKE_THIS_TAG_INT, istatus);
+      MPI_Recv(&which_atom, 1, MPI_INT, 0, 
+	       TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
       
       myStatus = 1;
       local_index=-1;        
@@ -517,16 +585,19 @@ void DumpWriter::writeFinal(){
       }
       if (local_index != -1) {
 
+	atoms[local_index]->getPos(pos);
+	atoms[local_index]->getVel(vel);
+
 	//format the line
 	sprintf( tempBuffer,
 		 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
 		 atoms[local_index]->getType(),
-		 atoms[local_index]->getX(),
-		 atoms[local_index]->getY(),
-		 atoms[local_index]->getZ(),
-		 atoms[local_index]->get_vx(),
-		 atoms[local_index]->get_vy(),
-		 atoms[local_index]->get_vz()); // check here.
+		 pos[0],
+		 pos[1],
+		 pos[2],
+		 vel[0],
+		 vel[1],
+		 vel[2]); // check here.
 	strcpy( writeLine, tempBuffer );
 	
 	if( atoms[local_index]->isDirectional() ){
@@ -559,10 +630,10 @@ void DumpWriter::writeFinal(){
 	strcpy( writeLine, "Hello, I'm an error.\n");
       }
 
-      MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, 
-			   TAKE_THIS_TAG_CHAR);
-      MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, 
-			    TAKE_THIS_TAG_INT);
+      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, 
+	       TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
+      MPI_Send( &myStatus, 1, MPI_INT, 0, 
+		TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
     }
   }
   finalOut.flush();
@@ -585,8 +656,8 @@ void dWrite::nodeZeroError( void ){
   
   myStatus = 0;
   for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
-    MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, 
-			  TAKE_THIS_TAG_INT);
+    MPI_Send( &myStatus, 1, MPI_INT, j, 
+	      TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
   }