--- trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2003/07/09 22:14:06	586
+++ trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2003/07/21 21:27:40	643
@@ -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
 
@@ -84,7 +84,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_simn
   char *parseErr;
   int procIndex;
   double boxMat[9];
-  
+  double theBoxMat3[3][3];
 
   simnfo = the_simnfo;
 
@@ -130,9 +130,12 @@ void InitializeFromFile :: read_xyz( SimInfo* the_simn
     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 );
 
+
   for( i=0; i < n_atoms; i++){
     
     eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
@@ -301,7 +304,11 @@ 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 );
 
    
 #endif
@@ -540,8 +547,15 @@ 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 );
+  }
+  simnfo->setTime( atof( foo ) );
 
   // get the Hx vector