How to merge structure with LAMMPS

LAMMPS LAMMPS General Discussion
1

I want to put an organic molecule in-between the bilayer graphene with the Al2O3/Bilayer Graphene/Al2O3 structure. These are the structure file of the organic molecule and the input parameter settings.
data.lmp (5.0 KB)
in.combination (488 Bytes)
This is the structure of the Al2O3/Bilayer Graphene/Al2O3

 # LAMMPS data file written by OVITO Basic 3.10.4
 
 85080 atoms
  4 atom types
 
 0.0 24.7284 xlo xhi
 0.0 23.795 ylo yhi
 0.0 1231.6781 zlo zhi
 
 Masses
 
 1 15.9994  # O
 2 26.981538  # Al
  3 12.0107  # C 
  4 12.0107  # C 
 
 Atoms  # charge
 
           1           1   0.0000000000000000        0.0000000000000000        1.4562539999999999        607.09167213379999
......
......
......
       85080           4   0.0000000000000000        23.354564281199998        19.036000000000001        619.59689988310004

After I launched the calculation, I obtain the following error message.

LAMMPS (17 Apr 2024)
ERROR: No bonds allowed with atom style charge (../read_data.cpp:221)
Last command: read_data algral.lmp extra/atom/types 5 extra/bond/types 5 extra/angle/types 7 extra/dihedral/types 6 extra/improper/types 1                     extra/bond/per/atom 100 extra/angle/per/atom 100 extra/dihedral/per/atom 100 extra/improper/per/atom 100
srun: error: b09r4n19: tasks 0-31: Exited with exit code 1
srun: launch/slurm: _step_signal: Terminating StepId=17337968.0

Would anyone please tell me how to correct the input file so as to put the organic molecule in-between the bilayer graphene?

Thank you in advance.

Kieran

2

You should change the atom_style from atomic to full.

The reason is that you have charges, bonds, angles and dihedrals in your system. Have a careful read of the manual atom_style command — LAMMPS documentation especially the table with the Atom style attributes.

Hope that helps

1 Like
3

Thank you for the reply.

Yes, the problem was solved after I switched to the full atom style.