[lammps-users] pizza atom limit?

Hi All:

I've been using pizza.py to convert my LAMMPS.dump files into ensight format. I've been successfully using the script below for a variety of simulations

# simple test of ensight tool ########

d = dump("au_bignw_push.dump")
d.map(1,"id",2,"x", 3,"y", 4,"z", 5, "type", 6, "energy")
e = ensight(d)
e.change = 1
e.maxtype = 1

print "all done ... type CTRL-D to exit Pizza.py"

Hi All:


which seems to imply that I ran out of memory for some reason. I
checked my memory as Pizza was converting; I have 16 GB of RAM on a G5
Mac, and not more than 6 GB was utilized when the memory error occurred.

Does anyone have any suggestions as to how I might be able to avoid

have you checked whether your python compile is 32-bit or 64-bit?

i remember from discussions with the VMD developers, that several
"older" python versions had serious problems in 64-bit mode. also
there were problems with MacOS versions not being very reliable,
so that VMD versions for MacOS with python included were only available
as inofficial builds. the official versions were built without...


The dump tool in Pizza.py can read a dump file one snapshot
at a time in a loop that you write in Python. See the examples/test_dump.py
file for a simple example. Inside that loop you can invoke the
ensight tool on one snapshot. You can also discard old snapshots
as you read them (see dump.delete()).

Essentially you would then process your snapshots one at a time,
w/out requiring them all to be in memory.


Hi Steve:

Thanks for your tip. I was studying the dump command on the LAMMPS website, and wrote the following script:

You need d = dump(file,0) as the 1st line which will
not start to read the file until you issue d.next() one
shapshot at a time. The d.iterator is different, it
is for looping over snapshots once the whole dump file
is read in (e.g. for viz).