--- trunk/mdtools/md_code/InitializeFromFile.cpp	2002/12/13 17:59:48	208
+++ trunk/mdtools/md_code/InitializeFromFile.cpp	2002/12/13 17:59:52	209
@@ -59,20 +59,16 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
 
   int i; // loop counter
 
+  const int BUFFERSIZE = 2000; // size of the read buffer
   int n_atoms; // the number of atoms
-  char read_buffer[2000]; //the line buffer for reading 
+  char read_buffer[BUFFERSIZE]; //the line buffer for reading 
 #ifdef IS_MPI
-  char send_buffer[2000];
+  char send_buffer[BUFFERSIZE];
 #endif
 
   char *eof_test; // ptr to see when we reach the end of the file 
-  char *foo; // the pointer to the current string token 
+  char *parseErr;
 
-  double rx, ry, rz; // position place holders
-  double vx, vy, vz; // velocity placeholders
-  double q[4]; // the quaternions
-  double jx, jy, jz; // angular velocity placeholders;
-  double qSqr, qLength; // needed to normalize the quaternion vector.
 
   entry_plug = the_entry_plug
 
@@ -80,10 +76,14 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
 #ifndef IS_MPI
   eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
   if( eof_test == NULL ){
-    std::cerr << "error reading 1st line of" << c_in_name << "\n";
+    sprintf( painCave.errMsg,
+	     "InitializeFromFile error: error reading 1st line of \"%s\"\n",
+	     c_in_name );
+    painCave.isFatal = 1;
+    simError();
   }
 
-  (void)sscanf(read_buffer, "%d", &n_atoms);
+  n_atoms = atoi( read_buffer );
 
   Atom **atoms = entry_plug->atoms;
   DirectionalAtom* dAtom;
@@ -120,205 +120,13 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
       simError();
     }
 
-    foo = strtok(read_buffer, " ,;\t");
     
-    // check the atom name to the current atom
-
-    if( strcmp( foo, atoms[i]->getType() ) ){
-      sprintf( painCave.errMsg,
-	       "Initialize from file error. Atom %s at index %d "
-	       "in file %s does not"
-	       " match the BASS atom %s.\n",
-	       foo, i, c_in_name, atoms[i]->getType() );
+    parseErr = parseDumpLine( read_buffer, i );
+    if( parseErr != NULL ){
+      strcpy( painCave.errMsg, parseErr );
       painCave.isFatal = 1;
       simError();
-    }
-    
-    // get the positions
-
-    foo = strtok(NULL, " ,;\t");
-    if(foo == NULL){
-      sprintf( painCave.errMsg,
-	       "error in reading postition x from %s\n"
-	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-      painCave.isFatal = 1;
-      simError();
-    }
-    (void)sscanf( foo, "%lf", &rx );
-   
-    foo = strtok(NULL, " ,;\t");
-    if(foo == NULL){
-      sprintf( painCave.errMsg,
-	       "error in reading postition y from %s\n"
-	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-      painCave.isFatal = 1;
-      simError();
-    }
-    (void)sscanf( foo, "%lf", &ry );
-     
-    foo = strtok(NULL, " ,;\t");
-    if(foo == NULL){
-      sprintf( painCave.errMsg,
-	       "error in reading postition z from %s\n"
-	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-      painCave.isFatal = 1;
-      simError();
-    }
-    (void)sscanf( foo, "%lf", &rz );
-    
-    // get the velocities
-
-    foo = strtok(NULL, " ,;\t");
-    if(foo == NULL){
-      sprintf( painCave.errMsg,
-	       "error in reading velocity x from %s\n"
-	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-      painCave.isFatal = 1;
-      simError();
-    }
-    (void)sscanf( foo, "%lf", &vx );
-    
-    foo = strtok(NULL, " ,;\t");
-    if(foo == NULL){
-      sprintf( painCave.errMsg,
-	       "error in reading velocity y from %s\n"
-	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-      painCave.isFatal = 1;
-      simError();
-    }
-    (void)sscanf( foo, "%lf", &vy );
-    
-    foo = strtok(NULL, " ,;\t");
-    if(foo == NULL){
-      sprintf( painCave.errMsg,
-	       "error in reading velocity z from %s\n"
-	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-      painCave.isFatal = 1;
-      simError();
-    }
-    (void)sscanf( foo, "%lf", &vz );
-    
-    
-    // get the quaternions
-    
-    if( atoms[i]->isDirectional() ){
-      
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	sprintf(painCave.errMsg,
-		"error in reading quaternion 0 from %s\n"
-		"natoms  = %d, index = %d\n",
-		c_in_name, n_atoms, i );
-	painCave.isFatal = 1;
-	simError();
-      }
-      (void)sscanf( foo, "%lf", &q[0] );
-      
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	sprintf( painCave.errMsg,
-		 "error in reading quaternion 1 from %s\n"
-		 "natoms  = %d, index = %d\n",
-		 c_in_name, n_atoms, i );
-	painCave.isFatal = 1;
-	simError();
-      }
-      (void)sscanf( foo, "%lf", &q[1] );
-      
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	sprintf( painCave.errMsg,
-		 "error in reading quaternion 2 from %s\n"
-		 "natoms  = %d, index = %d\n",
-		 c_in_name, n_atoms, i );
-	painCave.isFatal = 1;
-	simError();
-      }
-      (void)sscanf( foo, "%lf", &q[2] );
-      
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	sprintf( painCave.errMsg,
-		 "error in reading quaternion 3 from %s\n"
-		 "natoms  = %d, index = %d\n",
-		 c_in_name, n_atoms, i );
-	painCave.isFatal = 1;
-	simError();
-      }
-      (void)sscanf( foo, "%lf", &q[3] );
-      
-      // get the angular velocities
-      
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	sprintf( painCave.errMsg,
-		 "error in reading angular momentum jx from %s\n"
-		 "natoms  = %d, index = %d\n",
-		 c_in_name, n_atoms, i );
-	painCave.isFatal = 1;
-	simError();
-      }
-      (void)sscanf( foo, "%lf", &jx );
-      
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	sprintf( painCave.errMsg,
-		 "error in reading angular momentum jy from %s\n"
-		 "natoms  = %d, index = %d\n",
-		 c_in_name, n_atoms, i );
-	painCave.isFatal = 1;
-	simError();
-      }
-      (void)sscanf( foo, "%lf", &jy );
-      
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	sprintf( painCave.errMsg,
-		 "error in reading angular momentum jz from %s\n"
-		 "natoms  = %d, index = %d\n",
-		 c_in_name, n_atoms, i );
-	painCave.isFatal = 1;
-	simError();
-      }
-      (void)sscanf( foo, "%lf", &jz );
-      
-      dAtom = ( DirectionalAtom* )atoms[i];
-
-      // check that the quaternion vector is normalized
-
-      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
-      
-      qLength = sqrt( qSqr );
-      q[0] = q[0] / qLength;
-      q[1] = q[1] / qLength;
-      q[2] = q[2] / qLength;
-      q[3] = q[3] / qLength;
-      
-      dAtom->setQ( q );
-      
-      // add the angular velocities
-
-      dAtom->setJx( jx );
-      dAtom->setJy( jy );
-      dAtom->setJz( jz );
-    }
-    
-    // add the positions and velocities to the atom
-    
-    atoms[i]->setX( rx );
-    atoms[i]->setY( ry );
-    atoms[i]->setZ( rz );
-    
-    atoms[i]->set_vx( vx );
-    atoms[i]->set_vy( vy );
-    atoms[i]->set_vz( vz );
-    
+    }    
   }
 
 
@@ -337,12 +145,12 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
       simError();
     }
     
-    (void)sscanf(read_buffer, "%d", &n_atoms);
+    n_atoms = atoi( read_buffer );
     
     Atom **atoms = entry_plug->atoms;
     DirectionalAtom* dAtom;
     
-    if( n_atoms != entry_plug->n_atoms ){
+    if( n_atoms != entry_plug->mpiSim->getTotAtoms() ){
       sprintf( painCave.errMsg,
 	       "Initialize from File error. %s n_atoms, %d, "
 	       "does not match the BASS file's n_atoms, %d.\n",
@@ -361,6 +169,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
       simError();
     }
   }
+
   for( i=0; i < n_atoms; i++){
     
     eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
@@ -373,208 +182,227 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
       painCave.isFatal = 1;
       simError();
     }
-
-    foo = strtok(read_buffer, " ,;\t");
     
-    // check the atom name to the current atom
-
-    if( strcmp( foo, atoms[i]->getType() ) ){
-      sprintf( painCave.errMsg,
-	       "Initialize from file error. Atom %s at index %d "
-	       "in file %s does not"
-	       " match the BASS atom %s.\n",
-	       foo, i, c_in_name, atoms[i]->getType() );
+    parseErr = parseDumpLine( read_buffer, i );
+    if( parseErr != NULL ){
+      strcpy( painCave.errMsg, parseErr );
       painCave.isFatal = 1;
       simError();
-    }
+    }    
+  }
+#endif
+}
+
+
+char* IntitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
+
+  char *foo; // the pointer to the current string token 
+  
+  double rx, ry, rz; // position place holders
+  double vx, vy, vz; // velocity placeholders
+  double q[4]; // the quaternions
+  double jx, jy, jz; // angular velocity placeholders;
+  double qSqr, qLength; // needed to normalize the quaternion vector.
+  
+  Atom **atoms = entry_plug->atoms;
+  DirectionalAtom* dAtom;
+  
+  int n_atoms;
+
+#ifdef IS_MPI
+  n_atoms = entry_plug->mpiSim->getTotAtoms();
+#else
+  n_atoms = entry_plug->n_atoms;
+#endi // is_mpi
+
+
+  // set the string tokenizer
+  
+  foo = strtok(readLine, " ,;\t");
+  
+  // check the atom name to the current atom
+  
+  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
+    sprintf( painCave.errMsg,
+	     "Initialize from file error. Atom %s at index %d "
+	     "in file %s does not"
+	     " match the BASS atom %s.\n",
+	     foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
+    return strdup( painCave.errMsg );
+  }
     
-    // get the positions
+  // get the positions
+
+  foo = strtok(NULL, " ,;\t");
+  if(foo == NULL){
+    sprintf( painCave.errMsg,
+	     "error in reading postition x from %s\n"
+	     "natoms  = %d, index = %d\n",
+	     c_in_name, n_atoms, atomIndex );
+    return strdup( painCave.errMsg );
+  }
+  rx = atof( foo );
+   
+  foo = strtok(NULL, " ,;\t");
+  if(foo == NULL){
+    sprintf( painCave.errMsg,
+	     "error in reading postition y from %s\n"
+	     "natoms  = %d, index = %d\n",
+	     c_in_name, n_atoms, atomIndex );
+    return strdup( painCave.errMsg );
+  }
+  ry = atof( foo );
+     
+  foo = strtok(NULL, " ,;\t");
+  if(foo == NULL){
+    sprintf( painCave.errMsg,
+	     "error in reading postition z from %s\n"
+	     "natoms  = %d, index = %d\n",
+	     c_in_name, n_atoms, atomIndex );
+    return strdup( painCave.errMsg );
+  }
+  rz = atof( foo );    
 
+
+  // get the velocities
+
+  foo = strtok(NULL, " ,;\t");
+  if(foo == NULL){
+    sprintf( painCave.errMsg,
+	     "error in reading velocity x from %s\n"
+	     "natoms  = %d, index = %d\n",
+	     c_in_name, n_atoms, atomIndex );
+    return strdup( painCave.errMsg );
+  }
+  vx = atof( foo );
+    
+  foo = strtok(NULL, " ,;\t");
+  if(foo == NULL){
+    sprintf( painCave.errMsg,
+	     "error in reading velocity y from %s\n"
+	     "natoms  = %d, index = %d\n",
+	     c_in_name, n_atoms, atomIndex );
+    return strdup( painCave.errMsg );
+  }
+  vy = atof( foo );
+    
+  foo = strtok(NULL, " ,;\t");
+  if(foo == NULL){
+    sprintf( painCave.errMsg,
+	     "error in reading velocity z from %s\n"
+	     "natoms  = %d, index = %d\n",
+	     c_in_name, n_atoms, atomIndex );
+    return strdup( painCave.errMsg );
+  }
+  vz = atof( foo );
+    
+    
+  // get the quaternions
+    
+  if( atoms[atomIndex]->isDirectional() ){
+      
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
+      sprintf(painCave.errMsg,
+	      "error in reading quaternion 0 from %s\n"
+	      "natoms  = %d, index = %d\n",
+	      c_in_name, n_atoms, atomIndex );
+      return strdup( painCave.errMsg );
+    }
+    q[0] = atof( foo );
+      
+    foo = strtok(NULL, " ,;\t");
+    if(foo == NULL){
       sprintf( painCave.errMsg,
-	       "error in reading postition x from %s\n"
+	       "error in reading quaternion 1 from %s\n"
 	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-      painCave.isFatal = 1;
-      simError();
+	       c_in_name, n_atoms, atomIndex );
+      return strdup( painCave.errMsg );
     }
-    (void)sscanf( foo, "%lf", &rx );
-   
+    q[1] = atof( foo );
+      
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
       sprintf( painCave.errMsg,
-	       "error in reading postition y from %s\n"
+	       "error in reading quaternion 2 from %s\n"
 	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-      painCave.isFatal = 1;
-      simError();
+	       c_in_name, n_atoms, atomIndex );
+      return strdup( painCave.errMsg );
     }
-    (void)sscanf( foo, "%lf", &ry );
-     
+    q[2] = atof( foo );
+      
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
       sprintf( painCave.errMsg,
-	       "error in reading postition z from %s\n"
+	       "error in reading quaternion 3 from %s\n"
 	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-      painCave.isFatal = 1;
-      simError();
+	       c_in_name, n_atoms, atomIndex );
+      return strdup( painCave.errMsg );
     }
-    (void)sscanf( foo, "%lf", &rz );
-    
-    // get the velocities
-
+    q[3] = atof( foo );
+      
+    // get the angular velocities
+      
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
       sprintf( painCave.errMsg,
-	       "error in reading velocity x from %s\n"
+	       "error in reading angular momentum jx from %s\n"
 	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-      painCave.isFatal = 1;
-      simError();
+	       c_in_name, n_atoms, atomIndex );
+      return strdup( painCave.errMsg );
     }
-    (void)sscanf( foo, "%lf", &vx );
-    
+    jx = atof( foo );
+      
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
       sprintf( painCave.errMsg,
-	       "error in reading velocity y from %s\n"
+	       "error in reading angular momentum jy from %s\n"
 	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-      painCave.isFatal = 1;
-      simError();
+	       c_in_name, n_atoms, atomIndex );
+      return strdup( painCave.errMsg );
     }
-    (void)sscanf( foo, "%lf", &vy );
-    
+    jy = atof(foo );
+      
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
       sprintf( painCave.errMsg,
-	       "error in reading velocity z from %s\n"
+	       "error in reading angular momentum jz from %s\n"
 	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-      painCave.isFatal = 1;
-      simError();
+	       c_in_name, n_atoms, atomIndex );
+      return strdup( painCave.errMsg );
     }
-    (void)sscanf( foo, "%lf", &vz );
-    
-    
-    // get the quaternions
-    
-    if( atoms[i]->isDirectional() ){
+    jz = atof( foo );
       
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	sprintf(painCave.errMsg,
-		"error in reading quaternion 0 from %s\n"
-		"natoms  = %d, index = %d\n",
-		c_in_name, n_atoms, i );
-	painCave.isFatal = 1;
-	simError();
-      }
-      (void)sscanf( foo, "%lf", &q[0] );
-      
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	sprintf( painCave.errMsg,
-		 "error in reading quaternion 1 from %s\n"
-		 "natoms  = %d, index = %d\n",
-		 c_in_name, n_atoms, i );
-	painCave.isFatal = 1;
-	simError();
-      }
-      (void)sscanf( foo, "%lf", &q[1] );
-      
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	sprintf( painCave.errMsg,
-		 "error in reading quaternion 2 from %s\n"
-		 "natoms  = %d, index = %d\n",
-		 c_in_name, n_atoms, i );
-	painCave.isFatal = 1;
-	simError();
-      }
-      (void)sscanf( foo, "%lf", &q[2] );
-      
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	sprintf( painCave.errMsg,
-		 "error in reading quaternion 3 from %s\n"
-		 "natoms  = %d, index = %d\n",
-		 c_in_name, n_atoms, i );
-	painCave.isFatal = 1;
-	simError();
-      }
-      (void)sscanf( foo, "%lf", &q[3] );
-      
-      // get the angular velocities
-      
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	sprintf( painCave.errMsg,
-		 "error in reading angular momentum jx from %s\n"
-		 "natoms  = %d, index = %d\n",
-		 c_in_name, n_atoms, i );
-	painCave.isFatal = 1;
-	simError();
-      }
-      (void)sscanf( foo, "%lf", &jx );
-      
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	sprintf( painCave.errMsg,
-		 "error in reading angular momentum jy from %s\n"
-		 "natoms  = %d, index = %d\n",
-		 c_in_name, n_atoms, i );
-	painCave.isFatal = 1;
-	simError();
-      }
-      (void)sscanf( foo, "%lf", &jy );
-      
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	sprintf( painCave.errMsg,
-		 "error in reading angular momentum jz from %s\n"
-		 "natoms  = %d, index = %d\n",
-		 c_in_name, n_atoms, i );
-	painCave.isFatal = 1;
-	simError();
-      }
-      (void)sscanf( foo, "%lf", &jz );
-      
-      dAtom = ( DirectionalAtom* )atoms[i];
+    dAtom = ( DirectionalAtom* )atoms[atomIndex];
 
-      // check that the quaternion vector is normalized
+    // check that the quaternion vector is normalized
 
-      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
+    qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
       
-      qLength = sqrt( qSqr );
-      q[0] = q[0] / qLength;
-      q[1] = q[1] / qLength;
-      q[2] = q[2] / qLength;
-      q[3] = q[3] / qLength;
+    qLength = sqrt( qSqr );
+    q[0] = q[0] / qLength;
+    q[1] = q[1] / qLength;
+    q[2] = q[2] / qLength;
+    q[3] = q[3] / qLength;
       
-      dAtom->setQ( q );
+    dAtom->setQ( q );
       
-      // add the angular velocities
+    // add the angular velocities
 
-      dAtom->setJx( jx );
-      dAtom->setJy( jy );
-      dAtom->setJz( jz );
-    }
+    dAtom->setJx( jx );
+    dAtom->setJy( jy );
+    dAtom->setJz( jz );
+  }
     
-    // add the positions and velocities to the atom
+  // add the positions and velocities to the atom
     
-    atoms[i]->setX( rx );
-    atoms[i]->setY( ry );
-    atoms[i]->setZ( rz );
+  atoms[atomIndex]->setX( rx );
+  atoms[atomIndex]->setY( ry );
+  atoms[atomIndex]->setZ( rz );
     
-    atoms[i]->set_vx( vx );
-    atoms[i]->set_vy( vy );
-    atoms[i]->set_vz( vz );
-    
-  }
-#endif
-}
+  atoms[atomIndex]->set_vx( vx );
+  atoms[atomIndex]->set_vy( vy );
+  atoms[atomIndex]->set_vz( vz );
 
-char* IntitializeFromFile::parseDumpLine(char* readLine);
+  return NULL;
+}