Dear LAMMPS users,
I am trying to set up a GCMC, and eventually a GCMC/NVT grand-canonical calculation. I am using ReaxFF with USER/ReaxC on a graphene oxide system with large defects, and trying to insert C atoms into system with `fix gcmc’ to model healing of the defects. I understand that this is not the typical use case of this fix, all the examples I have seen are prepared to study adsorption of gas molecules etc. So, my first -or perhaps zeroth- question is, do you think it wouldn’t be wise to try using GCMC to study a problem like this?
I use the following input file, and my system (read by read_data data.in command) has no obvious problems as it runs well with fix nvt. However, when I try to run the appended input for GCMC calculation just hangs for hours. It creates the dump file writing out the initial coordinates, it prints outs the thermo line only for the first step, but does nothing else. Am I doing anything wrong here?
Finally, when I uncomment the overlap_cutoff 0.6 part, calculation immediately crashes with a segmentation fault. My feeling is that the two problems are related, but I don’t have any clues - as such, I would appreciate any help!
I am using the latest stable LAMMPS version on a supercomputer, and running the job on a single node, full 16 processors.
Best,
Sencer
Postdoctoral Fellow
Department of Chemistry
Princeton University
Dear LAMMPS users,
I am trying to set up a GCMC, and eventually a GCMC/NVT grand-canonical
calculation. I am using ReaxFF with USER/ReaxC on a graphene oxide system
with large defects, and trying to insert C atoms into system with `fix gcmc'
to model healing of the defects. I understand that this is not the typical
use case of this fix, all the examples I have seen are prepared to study
adsorption of gas molecules etc. So, my first -or perhaps zeroth- question
is, do you think it wouldn't be wise to try using GCMC to study a problem
like this?
I use the following input file, and my system (read by read_data data.in
command) has no obvious problems as it runs well with fix nvt. However, when
I try to run the appended input for GCMC calculation just hangs for hours.
It creates the dump file writing out the initial coordinates, it prints outs
the thermo line only for the first step, but does nothing else. Am I doing
anything wrong here?
Finally, when I uncomment the overlap_cutoff 0.6 part, calculation
immediately crashes with a segmentation fault. My feeling is that the two
problems are related, but I don't have any clues - as such, I would
appreciate any help!
I am using the latest stable LAMMPS version on a supercomputer, and running
the job on a single node, full 16 processors.
first step you need to do, is to try the same input with the latest
development version in order to verify that your issue is not already
solved.
if the issue persists, please also provide the data file and the
potential file, so that a developer can try to reproduce it and track
down the origin of the segfault/hang.
axel.
There are known problems with using GCMC with USER-REAXC. You should try Kokkos ReaxFF instead, it is more memory robust and others have had success with that.
Stan
Axel & Stan,
Thank you for responding. Compiling with Kokkos (OMP) solved the problem at least when I run without overlap_cutoff. This option still causes a seg fault immediately - both with dev and stable versions.
Perhaps I should open another thread but: I cannot use threading with Kokkos even a simple fix nve run. I add -k on t 2 -sf kk to the command line arguments, and it hangs indefinitely. I was able to run only with -k on t 1 -sf kk. Do I need anything else to do so?
I will try to reproduce the two problems with a smaller system and send the data files etc. I just wanted to give a heads up.
Best,
Sencer
Axel & Stan,
Thank you for responding. Compiling with Kokkos (OMP) solved the problem at
least when I run without `overlap_cutoff`. This option still causes a seg
fault immediately - both with dev and stable versions.
not here. i can add the flag to any of the existing gcmc input
examples and it works fine.
Perhaps I should open another thread but: I cannot use threading with Kokkos
even a simple `fix nve` run. I add `-k on t 2 -sf kk` to the command line
arguments, and it hangs indefinitely. I was able to run only with `-k on t 1
-sf kk`. Do I need anything else to do so?
please prefix your command line with: gdb --args
and when gdb has launched, type: run
let it run for a bit until you are certain it is hung, then hit CTRL-C
and type: where
and send us the screen output. that will tell in which subroutine it hangs.
for the segfault, please do the same thing. after lammps has
segfaulted, type where and e-mail us the stack trace.
axel.
Sencer,
You also can build the KOKKOS package with Makefile.kokkos_mpi_only and don't need to worry about threading. We are happy to look into this when you send us a reproducer input deck.
Thanks,
Stan