new read_dump command

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1

HI all - with help from Tim Sirk (U Vermont) there
is now a new read_dump command, to allow
you to input atom coords and other properties from
a specified snapshot of a dump file. See the 1 Jun patch.

For now, just native LAMMPS dump files (atom, custom)
are supported, but folks who know the DCD,XTC,etc formats,
could hopefully add a reader for those, as a sibling
of the ReadDumpNative class. Contact the developers
if interested.

The next task is to use the ReadDump class as a kernel
in a "rerun" command, to let you do a pseudo-run by
looping over dump snapshots.

Steve

2

Hi,
this command works fine if number atoms < 1028
but reading in more leads to a segmentation fault.
So i tried to split my dump files to read them in seperately, but it
also didn't work, because it replaced earlier red in atoms, even for
different atom IDs and the replace keyword switched off.

Jörg

3

Hi,
this command works fine if number atoms < 1028
but reading in more leads to a segmentation fault.

please provide some example files that reproduce this.
i have been able to use rerun and read_dump with much
more atoms. there is likely some issue in your input.

So i tried to split my dump files to read them in seperately, but it
also didn't work, because it replaced earlier red in atoms, even for
different atom IDs and the replace keyword switched off.

it is not clear what you are trying to say here.
please rephrase.

thanks,
     axel.

4

I tried different dump files, some created by my one, but also some
written by LAMMPS.
Here the output of LAMMPS:

mdlat.out_4904_CS.dump (189 KB)

5

the dump file alone is useless. where is the matching input?

axel.

6

I'm sorry, it was just a simple read_dump add line:

7

> I tried different dump files, some created by my one, but also some
> written by LAMMPS.

the dump file alone is useless. where is the matching input?

axel.

I'm sorry, it was just a simple read_dump add line:

this is a bad idea. the way to use read_dump
and rerun is that you first set up a regular run
with the system you want to run and then
overwrite the coordinates from the dump.

e.g. use a restart or a data file and then
use read_dump or rerun.

axel.

8

to explain a bit more in detail:
to make the "add" flag of "read_dump" work,
you have to have at least one atom created
in one way or another. this atom creation will
do certain one-time initialization steps that
are required by read_dump.

so, in principle, you can make your input work
by adding one single line:

create_atoms 1 single 1.0 1.0 1.0

axel.