Hi. I am using the April 20th 2012 version of LAMMPS and having difficulty with the delete_bonds command. I have an initial data file with 5 atom types, 252750 atoms, and 252679 bonds. 68 of the atoms have type 1; I delete them and their associated bonds using the command sequence
group todel type 1
delete_bonds todel bond 1 any remove
group todel type 1
delete_atoms group todel
I then run a script for PPA analysis; the script is attached (PPAscript.goodinserialbadinparallel). In serial this generates output
PPAscript.goodinserialbadinparallel (1.37 KB)
hi rob,
what happens, if you put a
run 0
right before deleting the bonds?
also, can you try ramping up the
value for
communicate cutoff
to make sure that bonded atoms
are properly communicated in case
of having a short non-bonded cutoff.
if the problem persist, it would probably
be best to try and come up with a minimal
test system and post all necessary files
in order to do some proper debugging.
thanks,
axel.
Hi, Axel. The communicate cutoff worked, and the 'run 0' was not
necessary... after adding a communicate command right before deleting the
bonds so the relevant part of the script now reads
read_data data.chain.Rob
communicate single cutoff 1.5
group todel type 1
delete_bonds todel bond 1 any remove
group todel type 1
delete_atoms group todel,
it now runs fine in parallel, and this was not a bug 
Thanks!
Rob