Dump / Data file Processing

I just recently discovered awk and am now reading up on its capabilities, and was wondering if any lammps users use awk/gawk in the creation and or processing/manipulation of dump files, data files etc.

Any general guidance, preferences, and what you consider to be pros and cons based your experiences would be appreciated.

I was also recently trying to learn python in connection with the pizza.py tools, and wondered if some lammps users had more of a preference for either one of these two choices when manipulating lammps input and output data.

respectfully,

Hi

----- Tools for building DATA files ----

There are now days two large, full-featured programs written
specifically for building lammps DATA files:

1) Moltemplate is a complete molecule builder which can be used to
prepare both lammps data files and input scripts:

http://www.moltemplate.org/
It was designed for building coarse-grained biopolymers.
(There is a program to extract molecules from existing lammps
data&input files and convert them to moltemplate format.)

2) Topotools is a tool for building and converting lammps DATA files,
and it has some important features moltemplate lacks (like a graphical
interface, the ability to solvate a molecule, or assign bonds by
distance, or use for-loops and conditional branching).

http://sites.google.com/site/akohlmey/software/topotools
http://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-1

After topotools is done, you must write your own input script
manually, but this is usually not a great deal of work (by
comparison).

3) Although not designed specifically for lammps, PACKMOL may be
useful for generating the initial coordinates for the atoms in your
system. It can generate files which can be read by either moltemplate
or topotools:

http://www.ime.unicamp.br/~martinez/packmol/

-------- For processing DUMP files: ----------

I'm not an expert, but pizza.py is probably the most useful program
for processing DUMP files.

VMD has plugins which can analyze data files, convert dump files to
other formats. (Once converted to other formats, there are many other
tools you can use to analyze a trajectory, which I know little about
unfortunately.)

Let me know if I left anything out.
I hope this answers your question.

    One last detail:
Any lammps DUMP file can be read at a later time by lammps and
quantities can be calculated from it. This is done using the "rerun"
command:
http://lammps.sandia.gov/doc/rerun.html
http://lammps.sandia.gov/doc/compute.html

Cheers!

Andrew

Thanks!