trim (option of rerun command) problem

Hello everyone,
I am trying to do some post-processing using rerun command. my dump file which rerun command reads, is made of a region I have defined on a previous run:

run.txt (5.99 KB)

rerun.txt (3.3 KB)


now when I try to do a new run using rerun command :

rerun conf-25eth-run.lammpstrj dump x y z box yes trim yes

trim keyword deletes the rest of the data file which is not matched with
dump file. (it actually deletes all atoms except those you have in the
defined region - "confined" here- so a post processing on those specific
atoms with maybe different settings can be done)
I get a "bond atom missing" error. I know the problem is some atoms of some
molecules in the boundaries are missed because they were not in the region
at the timestep of dumping and therefore vanished by "trim"!
to make sure this is the problem, I changed one of dump files and deleted
all atoms of incomplete molecules and the problem was solved.

any Idea how this can be fixed?

a) dump the entire system instead of subsets so you don't have to use
the trim option
b) take your favorite text editor and teach the read_dump command a
"trim mol" option that deletes *all* atoms of a molecule instead of
just one. you can have a look at the sources for the delete_atoms
command for inspiration, as it has been very recently been taught the
same thing.


thank you very much

Best regards