| 327 | 
  | 
  double pos[3]; // position place holders | 
| 328 | 
  | 
  double vel[3]; // velocity placeholders | 
| 329 | 
  | 
  double q[4]; // the quaternions | 
| 330 | 
< | 
  double jx, jy, jz; // angular velocity placeholders; | 
| 330 | 
> | 
  double ji[3]; // angular velocity placeholders; | 
| 331 | 
  | 
  double qSqr, qLength; // needed to normalize the quaternion vector. | 
| 332 | 
  | 
 | 
| 333 | 
  | 
  Atom **atoms = simnfo->atoms; | 
| 490 | 
  | 
               c_in_name, n_atoms, atomIndex ); | 
| 491 | 
  | 
      return strdup( painCave.errMsg ); | 
| 492 | 
  | 
    } | 
| 493 | 
< | 
    jx = atof( foo ); | 
| 493 | 
> | 
    ji[0] = atof( foo ); | 
| 494 | 
  | 
 | 
| 495 | 
  | 
    foo = strtok(NULL, " ,;\t"); | 
| 496 | 
  | 
    if(foo == NULL){ | 
| 500 | 
  | 
               c_in_name, n_atoms, atomIndex ); | 
| 501 | 
  | 
      return strdup( painCave.errMsg ); | 
| 502 | 
  | 
    } | 
| 503 | 
< | 
    jy = atof(foo ); | 
| 503 | 
> | 
    ji[1] = atof(foo ); | 
| 504 | 
  | 
 | 
| 505 | 
  | 
    foo = strtok(NULL, " ,;\t"); | 
| 506 | 
  | 
    if(foo == NULL){ | 
| 510 | 
  | 
               c_in_name, n_atoms, atomIndex ); | 
| 511 | 
  | 
      return strdup( painCave.errMsg ); | 
| 512 | 
  | 
    } | 
| 513 | 
< | 
    jz = atof( foo ); | 
| 513 | 
> | 
    ji[2] = atof( foo ); | 
| 514 | 
  | 
 | 
| 515 | 
  | 
    dAtom = ( DirectionalAtom* )atoms[atomIndex]; | 
| 516 | 
  | 
 | 
| 528 | 
  | 
 | 
| 529 | 
  | 
    // add the angular velocities | 
| 530 | 
  | 
 | 
| 531 | 
< | 
    dAtom->setJx( jx ); | 
| 532 | 
< | 
    dAtom->setJy( jy ); | 
| 533 | 
< | 
    dAtom->setJz( jz ); | 
| 531 | 
> | 
    dAtom->setJ( ji ); | 
| 532 | 
  | 
  } | 
| 533 | 
  | 
 | 
| 534 | 
  | 
  // add the positions and velocities to the atom |