--- trunk/OOPSE/libmdtools/DumpReader.cpp	2004/04/19 17:44:48	1119
+++ trunk/OOPSE/libmdtools/DumpReader.cpp	2004/06/11 17:16:21	1268
@@ -84,15 +84,10 @@ void DumpReader::scanFile( void ){
 
 void DumpReader::scanFile( void ){
 
-  int vectorSize;
-  int i, j, k;
+  int i, j;
   int lineNum = 0;
   char readBuffer[2000];
-  char* foo;
   fpos_t *currPos;
-  double time;
-
-
 
 #ifdef IS_MPI
   if( worldRank == 0 ){
@@ -176,7 +171,8 @@ void DumpReader :: readSet( int whichFrame ){
 
 void DumpReader :: readSet( int whichFrame ){
 
-   int i, j;
+  int i;
+  unsigned int j;
 
 #ifdef IS_MPI
   int done, which_node, which_atom; // loop counter
@@ -273,7 +269,9 @@ void DumpReader :: readSet( int whichFrame ){
   int *MolToProcMap = mpiSim->getMolToProcMap();
   int localIndex;
   int nCurObj;
+  int nitems;
 
+  nTotObjs = simnfo->getTotIntegrableObjects();
   haveError = 0;
   if (worldRank == 0) {
      fsetpos(inFile,  framePos[whichFrame]);
@@ -286,12 +284,12 @@ void DumpReader :: readSet( int whichFrame ){
       simError();
     }
 
-    nTotObjs = atoi( read_buffer );
+    nitems = atoi( read_buffer );
 
     // Check to see that the number of integrable objects  in the intial configuration file is the
     // same as declared in simBass.
 
-    if( nTotObjs != simnfo->getTotIntegrableObjects()){
+    if( nTotObjs != nitems){
       sprintf( painCave.errMsg,
 	       "DumpReadererror. %s n_atoms, %d, "
 	       "does not match the BASS file's n_atoms, %d.\n",
@@ -325,7 +323,7 @@ void DumpReader :: readSet( int whichFrame ){
       simError();
     }
 
-    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
+    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
       which_node = MolToProcMap[i];
       if(which_node == 0){
        //molecules belong to master node
@@ -354,7 +352,7 @@ void DumpReader :: readSet( int whichFrame ){
           
           if(haveError) nodeZeroError();
 
-          parseDumpLine(read_buffer, integrableObjects[i]);
+          parseDumpLine(read_buffer, integrableObjects[j]);
            
        }
 
@@ -363,10 +361,10 @@ void DumpReader :: readSet( int whichFrame ){
       else{
       //molecule belongs to slave nodes
 
-        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
+        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
 	       TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
       
-       for(j=0; j < integrableObjects.size(); j++){
+       for(j=0; j < nCurObj; j++){
         
           eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
           if(eof_test == NULL){
@@ -393,7 +391,17 @@ void DumpReader :: readSet( int whichFrame ){
   }
   else{
   //actions taken at slave nodes
-    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
+    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
+
+    parseErr = parseCommentLine( read_buffer, simnfo);
+
+    if( parseErr != NULL ){
+      strcpy( painCave.errMsg, parseErr );
+      haveError = 1;
+      simError();
+    }
+  
+    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
       which_node = MolToProcMap[i];
       
       if(which_node == worldRank){
@@ -411,8 +419,8 @@ void DumpReader :: readSet( int whichFrame ){
 
         nCurObj = integrableObjects.size();
         
-        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
-                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
+        MPI_Send(&nCurObj, 1, MPI_INT, 0,
+                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
 
         for(j = 0; j < integrableObjects.size(); j++){
 
@@ -604,6 +612,12 @@ char* DumpReader::parseDumpLine(char* readLine, StuntD
 
     qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
 
+    if (fabs(qSqr) < 1e-6) {
+      sprintf(painCave.errMsg,
+          "initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
+       return strdup(painCave.errMsg);
+    }
+
     qLength = sqrt( qSqr );
     q[0] = q[0] / qLength;
     q[1] = q[1] / qLength;
@@ -732,7 +746,7 @@ void DumpReader::nodeZeroError( void ){
   int j, myStatus;
 
   myStatus = 0;
-  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
+  for (j = 0; j < mpiSim->getNProcessors(); j++) {
     MPI_Send( &myStatus, 1, MPI_INT, j,
 	      TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
   }
@@ -748,4 +762,4 @@ void DumpReader::anonymousNodeDie( void ){
   MPI_Finalize();
   exit (0);
 }
-#endif
\ No newline at end of file
+#endif