Segmentation fault with hybrid ellipsoid peri molecular

LAMMPS LAMMPS Beginners
1

Dear Experts,

I try to run LAMMPS (version 23Jun2022) using: atom_style hybrid ellipsoid peri molecular for a toy system. The data file is:

LAMMPS data file for hybrid ellipsoid + peri + molecular

2 atoms
2 atom types
1 ellipsoids

0.0 10.0 xlo xhi
0.0 10.0 ylo yhi
0.0 10.0 zlo zhi

Masses

1 1.0
2 1.0

ID type x y z ellipsoidflag density volume molID

Atoms

1 1 1.0 1.0 1.0 1 1.0 1.0 1
2 1 2.0 2.0 2.0 0 1.0 1.0 2

Ellipsoids

1 1.0 1.0 1.0 1.0 0.0 0.0 0.0

And the lammps input file is:

units lj
atom_style hybrid ellipsoid peri molecular

read_data data.hybrid_example

pair_style zero 10.0
pair_coeff * *

neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes

fix 1 all nve/asphere

thermo 1
run 10

However, I always get error:

mpirun -np 2 lmp -in in.hybrid
LAMMPS (23 Jun 2022 - Update 4)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:133)
WARNING: Per-atom field rmass is used in multiple sub-styles; must be used consistently (src/atom_vec_hybrid.cpp:167)
Reading data file …
orthogonal box = (0 0 0) to (10 10 10)
[seurat:271768] *** Process received signal ***
[seurat:271768] Signal: Segmentation fault (11)
[seurat:271768] Signal code: Address not mapped (1)
[seurat:271768] Failing at address: (nil)
1 by 1 by 2 MPI processor grid
reading atoms …
[seurat:271768] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x76ba4ac45330]

If I use a single atom_style, either ellipsoid, or peri or molecular then it works fine. Also, the hybrid ellipsoid molecular works fine. The problem occurs if I include the style peri.

Thank you very much for any hints.

2

Hi,

Please read the guidelines and revise your post, your inputs are difficult to read. Also, note that:

are not specific to LAMMPS and therefore not very helpful here.

This is what a LAMMPS error message looks like (obtained using version 29Aug2024):

ERROR on proc 0: Fix nve/asphere requires extended particles (…/fix_nve_asphere.cpp:54)

which clearly states what the problem is.

Best,
Simon

3

You may want to use a more recent version also.

4

Thanks you so much. It works with the version 2024.

1 Like
5

Lesson: before complaining about a crash, always check with the latest version.

6

Thanks. In fact this hybrid worked well with the version 2017, but surprisingly doesn’t work with the version 2022, but then work again with 2024.