--- trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2003/07/09 22:14:06	586
+++ trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2003/07/22 16:41:08	644
@@ -69,7 +69,7 @@ InitializeFromFile :: ~InitializeFromFile( ){
 }
 
 
-void InitializeFromFile :: read_xyz( SimInfo* the_simnfo ){
+void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
 
   int i, j, done, which_node, which_atom; // loop counter
 
@@ -83,8 +83,9 @@ void InitializeFromFile :: read_xyz( SimInfo* the_simn
   char *eof_test; // ptr to see when we reach the end of the file 
   char *parseErr;
   int procIndex;
+  double currTime;
   double boxMat[9];
-  
+  double theBoxMat3[3][3];
 
   simnfo = the_simnfo;
 
@@ -123,16 +124,20 @@ void InitializeFromFile :: read_xyz( SimInfo* the_simn
     simError();
   }
 
-  parseErr = parseBoxLine( read_buffer, boxMat );
+  parseErr = parseBoxLine( read_buffer, boxMat, currTime );
   if( parseErr != NULL ){
     strcpy( painCave.errMsg, parseErr );
     painCave.isFatal = 1;
     simError();
   }
 
-  simnfo->setBoxM( boxMat );
+  for(i=0;i<3;i++)
+    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
 
+  simnfo->setBoxM( theBoxMat3 );
+  simnfo->setTime( currTime );
 
+
   for( i=0; i < n_atoms; i++){
     
     eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
@@ -207,7 +212,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_simn
       simError();
     }
     
-    parseErr = parseBoxLine( read_buffer, boxMat );
+    parseErr = parseBoxLine( read_buffer, boxMat, currTime );
     if( parseErr != NULL ){
       strcpy( painCave.errMsg, parseErr );
       haveError = 1;
@@ -215,6 +220,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_simn
     }
 
     MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
+    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
   
     if(haveError) nodeZeroError();
 
@@ -269,6 +275,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_simn
   } else {
     
     MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
+    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
 
     done = 0;
     while (!done) {
@@ -301,8 +308,13 @@ void InitializeFromFile :: read_xyz( SimInfo* the_simn
      
  // last  thing last, enable  fatalities.
   painCave.isEventLoop = 0;
-  simnfo->setBoxM( boxMat );
+
+  for(i=0;i<3;i++)
+    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
 
+  simnfo->setBoxM( theBoxMat3 );
+  simnfo->setTime( currTime );
+
    
 #endif
 }
@@ -532,7 +544,8 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 }
 
 
-char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9]){
+char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9],
+				       double &time ){
 
   char *foo; // the pointer to the current string token 
   int j;
@@ -540,8 +553,15 @@ char* InitializeFromFile::parseBoxLine(char* readLine,
   // set the string tokenizer
   
   foo = strtok(readLine, " ,;\t");
-  // ignore the first token which is the time stamp.
+  // set the timeToken.
 
+  if(foo == NULL){
+    sprintf( painCave.errMsg,
+	     "error in reading Time from %s\n",
+	     c_in_name );
+    return strdup( painCave.errMsg );
+  }
+  time = atof( foo );
 
   // get the Hx vector