[lammps-users] graphing output or log

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1

I'm curious how people go about graphing lammps thermo output. I use grace, and it chokes on the first bit of non-numeric output. Typically I copy the output to a working file and then crop it. But I'm sick of that, and it precludes graphing running data. At one time I considered altering the code to add a "#" to the beginning of all non-numeric stuff, but didn't want to redo it if it was broken in a new release. I'm wondering what everyone else does.
Matt

2

I'm curious how people go about graphing lammps thermo output. I use grace, and it chokes on the first bit of non-numeric output. Typically I copy the output to a working file and then crop it. But I'm sick of that, and it precludes graphing running data. At one time I considered altering the code to add a "#" to the beginning of all non-numeric stuff, but didn't want to redo it if it was broken in a new release. I'm wondering what everyone else does.

have you looked at Pizza.py?

axel.

3

Matt,

gnuplot works fine in most of the cases (unless you really have only a few
output lines).

Good luck,
Dan

4

For custom thermo outputs, I use gnuplot. You don't have to crop ,edit
or put "#'s" on the thermo log as long as you specify the column that
you are plotting.

for example, if you specify "thermo_style one" in your input script
then you can plot temperature vs. time using the gnuplot command:

plot "log.lammps" u 1:2

-Jan Michael

5

For custom thermo outputs, I use gnuplot. You don't have to crop ,edit
or put "#'s" on the thermo log as long as you specify the column that
you are plotting.

for example, if you specify "thermo_style one" in your input script
then you can plot temperature vs. time using the gnuplot command:

plot "log.lammps" u 1:2

-Jan Michael

6

I haven't look at Pizza.py. Haven't worked with gnuplot in a while either. I'll take a look at both. Thanks for all the replies.
Cheers,
Matt

7

You don't even need all of Pizza.py, just the log tool.
And it is included in LAMMPS, in the tools/python dir
(see the README file).

Basically the log tool (wrapped by the tools/python/log2txt.py
script) will do this in 2 lines:

lg = log("log.lammps")
lg.write("columns.txt")

and pull out all the numeric columns from your log file
into a txt file. This works across multiple runs, etc. You
can even do it from multiple log files.

Steve