I have been trying to use dump2xyz.py tool to convert dump output to xyz format.
I use this command:
./dump2xyz.py testatoms.txt 48016 6 100 100 100 at.xyz
And receive this error:...
I don't use dump2xyz.py, so I can not comment, but if you downloaded a
recent version of LAMMPS, it should come with "dump2data.py" script.
(It is currently located in the tools/moltemplate/src directory. If
not, download it at moltemplate.org. The current version is 0.43.)
You can use it this way.
dump2data.py -xyz < traj.lammpstrj > coords.xyz
More (hastily written) documentation is included below. Hopefully the
problems with dump2xyz.py will be fixed. If you are desperate, try
"dump2data.py" instead. I included the bits of documentation relevant
to generating xyz files. (You can use "-raw" instead of "-xyz" if you
prefer simple 3-column coordinate text format.)
"dump2data.py" was originally designed to convert dump files into
LAMMPS DATA format (for restarting a simulation from where it left
off). However it also reads and writes .XYZ and .RAW (simple 3-column
text format) files also. This script duplicates some of the tools in
pizza.py, but you don't have to learn python to use it. If you are
willing to learn a little python, pizza.py, can handle more general
dump files which might cause dump2data.py to crash (eg "atom_style
tri"). Unlike "dump2data.py", pizza.py is maintained by the lammps
team.
http://pizza.sandia.gov/doc/Manual.html
----- documentation for dump2data.py: ----
(rough draft)
General usage:
dump2data [old_data_file -xyz -raw -last -t time -tstart ta -tstop tb
-interval n -center -scale x -atomstyle style] < DUMP_FILE >
OUTPUT_FILE
----- examples -----
If your LAMMPS dump file is named "traj.lammpstrj", you can
extract the coordinates this way:
dump2data.py -xyz < traj.lammpstrj > traj.xyz
This generates a 3-column text file containing the xyz coordinates on
each line of each atom (sorted by atomid). If there are multiple
frames in the trajectory file, it will concatenate them together this
way:
8192
LAMMPS data from timestep 50000
1 -122.28 -19.2293 -7.93705
2 -121.89 -19.2417 -8.85591
3 -121.6 -19.2954 -7.20586
: : : :
8192
LAMMPS data from timestep 100000
1 -121.59 -20.3273 -2.0079
2 -122.2 -19.8527 -2.64669
3 -120.83 -19.7342 -2.2393
(When using the "-raw" argument to create simple 3-column .RAW files,
blank lines are used to delimit different frames in the trajectory.)
---- optional command line arguments ---
If you want to select a particular frame from the trajectory, use:
dump2data.py -xyz -t 10000 < traj.lammpstrj > coords.xyz
To select the most recent (complete) frame, use:
dump2data.py -xyz -last < traj.lammpstrj > coords.xyz
(If the last frame is incomplete, this script will attempt to use the
previous frame.)
If you want to select multiple frames, but there are too many frames
in your trajectory, you can run dump2data.py this way...
dump2data.py -xyz -interval 10000 < traj.lammpstrj > traj.xyz
...to indicate the desired interval between frames (it must be a multiple of
the save interval). You can also use "-tstart 500000 and "-tstop
1000000" arguments to limit the output to a particular range of time.
(500000-1000000 in this example).
--- creating DATA files ---
Although this may not have been a feature you were interested in,
"dump2data.py" can also create lammps DATA files. You must supply it
with an existing DATA file containing the correct number of atoms and
topology information.
Firstly, if you have a file containing only the coordinates of the
atoms (in sorted order), you can use "raw2data.py" to create a data
file with those atoms coordinates.
raw2data.py data_file < coords.raw > new_data_file
(Warning: "raw2data.py" is not a stand-alone script. Make sure
raw2data.py is located in the same directory with dump2data.py,
wherever that is.)
If your coordinates are stored in a DUMP file (eg "traj.lammpstrj"),
you can create a new data file this way:
dump2data.py -t 10000 data_file < traj.lammpstrj > new_file
Again, in this example, "10000" is the timestep for the frame you have
selected. You can use "-last" to select the last frame. (If you do
not specify the frame you want, multiple data files will be created.)
--- scaling and centering coordinates ---
-center
This will center the coordinates around the geometric center, so
that the average position of the atoms in each frame is located at the
origin. (This script attempts to pay attention to the periodic image
flags. As such, I think this script works with triclinic cells, but I
have not tested that feature carefully.)
-scale 1.6
This will multiply the coordinates by a constant (eg "1.6") (Please
email me if this fails with periodic image flags.)
---- limitations ----
Speed.
The program is somewhat slow, although it should be able to handle big
trajectories. If speed is important to you, you probably should write
your own custom script or use pizza.py which might be faster.
triclinic cells
Support for triclinic cells has been added, but not tested.
exotic atom_styles
This script was designed to work with point-like atoms, and it
extracts the x,y,z (and if present vx,vy,vz velocity) degrees of
freedom and (by default) copies it to the new data being created by
this script.
By default, this script assumes you are using "atom_style full".
If you are using some other atom style (eg "hybrid bond dipole"), then
you can try to run it this way:
dump2data.py -t 10000 \
-atomstyle "hybrid bond dipole" \
old_data_file < traj.lammpstrj > new_data_file
I have not tested this, and have no idea what will happen. (I suspect
that the script will not crash, but the dipole orientations will not
be updated.)
You can also customize the order columns you want to appear in that
file using -atomstyle "molid x y z atomid atomtype mux muy muz", but
again, I don't think the mux, muy, muz information in the new data
file will be accurate.
I also strongly suspect that "dump2data.py" does not currently work
with the "tri", "ellipsoid", and new "body" styles.
Again, try using pizza.py if you are simulating systems with exotic data types.
http://pizza.sandia.gov/doc/Manual.html
I hope this is useful to someone.
Cheers.
Andrew