raw2data.py replaces the coordinates of a LAMMPS data file with new coordinates.


Typical usage:

raw2data.py -atomstyle ATOMSTYLE FILE_OLD.data < COORDS.raw > FILE_NEW.data


This will create a new LAMMPS DATA file named "FILE_NEW.data" whose atom
coordinates are copied from the COORDS.raw file, but is otherwise identical
to the original DATA file (eg, "FILE_OLD.data").  The optional 
-atomstyle ATOMSTYLE argument tells raw2data.py about the format of the DATA 
file.  If not specified, the atom style is "full" by default.


Arguments:

ATOMSTYLE is a quoted string, such as "full" or "hybrid sphere dipole" indicating the format of the data file.  It can be any of the atom styles listed in the table at:
http://lammps.sandia.gov/doc/atom_style.html
...such as "angle", "bond", "charge", "full", "molecular", "dipole", "ellipsoid"
or any hybrid combination of these styles.

FILE_OLD.data
The second argument to raw2data.py is the name of a DATA file you want to read.
raw2data.py will replace the coordinates in the "Atoms" section of this file,
while preserving the rest of the data file.

COORDS.raw is a simple 3-column ASCII file containing the coordinates of the
atoms in your system.  It has a very simple format:
-122.28 -19.2293 -7.93705
-121.89 -19.2417 -8.85591
-121.6 -19.2954 -7.20586
-121.59 -20.3273 -2.0079
-122.2 -19.8527 -2.64669
-120.83 -19.7342 -2.2393
  :        :        :

The order of the atoms in this file should match the ATOM-ID number in the 
first column of the "Atoms" section of the FILE_OLD.data file.
(...I THINK...
 To be on the safe side, use a DATA file with the atoms in sorted order.)

Exotic atom styles:
   When using hybrid atom styles, you must enclose the argument in quotes, 
for example: "hybrid sphere dipole"

   Warning 1: I have not tested using raw2data.py with exotic (non-point-like) 
atom styles.  (I suspect that the script will not crash, but dipole orientations
and other internal degrees of freedom will not be updated.)

   Warning 2: "raw2data.py" is not a stand-alone script.  Make sure dump2data.py is located in the same directory with raw2data.py.

   Note: I have not tested it, but I suspect many of the other arguments that work with "dump2data.py", such as "-scale", and "-xyz" also work with raw2data.py.

Try using pizza.py if you are simulating systems with exotic data types.
http://pizza.sandia.gov/doc/Manual.html