--- trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2003/07/09 22:14:06	586
+++ trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2003/08/07 21:47:18	670
@@ -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
 }
@@ -311,8 +323,8 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 
   char *foo; // the pointer to the current string token 
   
-  double rx, ry, rz; // position place holders
-  double vx, vy, vz; // velocity placeholders
+  double pos[3]; // position place holders
+  double vel[3]; // velocity placeholders
   double q[4]; // the quaternions
   double jx, jy, jz; // angular velocity placeholders;
   double qSqr, qLength; // needed to normalize the quaternion vector.
@@ -365,7 +377,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  rx = atof( foo );
+  pos[0] = atof( foo );
    
   foo = strtok(NULL, " ,;\t");
   if(foo == NULL){
@@ -375,7 +387,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  ry = atof( foo );
+  pos[1] = atof( foo );
      
   foo = strtok(NULL, " ,;\t");
   if(foo == NULL){
@@ -385,7 +397,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  rz = atof( foo );    
+  pos[2] = atof( foo );    
 
 
   // get the velocities
@@ -398,7 +410,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  vx = atof( foo );
+  vel[0] = atof( foo );
     
   foo = strtok(NULL, " ,;\t");
   if(foo == NULL){
@@ -408,7 +420,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  vy = atof( foo );
+  vel[1] = atof( foo );
     
   foo = strtok(NULL, " ,;\t");
   if(foo == NULL){
@@ -418,7 +430,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  vz = atof( foo );
+  vel[2] = atof( foo );
     
     
   // get the quaternions
@@ -520,19 +532,15 @@ char* InitializeFromFile::parseDumpLine(char* readLine
     
   // add the positions and velocities to the atom
     
-  atoms[atomIndex]->setX( rx );
-  atoms[atomIndex]->setY( ry );
-  atoms[atomIndex]->setZ( rz );
-    
-  atoms[atomIndex]->set_vx( vx );
-  atoms[atomIndex]->set_vy( vy );
-  atoms[atomIndex]->set_vz( vz );
+  atoms[atomIndex]->setPos( pos );
+  atoms[atomIndex]->setVel( vel );
 
   return NULL;
 }
 
 
-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 +548,15 @@ 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