All pair coeffs are not set

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1

Dear Lammps Users,

I am simulating the system including metal (Ag) and organic. Interaction between Ag and organic atoms is LJ potential. For Ag, the potential is EAM. It includes 6 atom styles and the LJ parameters are in data file. However, it shows error “All pair coeffs are not set”.

Here is the input script.

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style charmm

pair_style hybrid lj/cut/coul/cut 10.0 8.0 eam

neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
special_bonds amber

read_data 2016712organic_Ag.data

pair_modify pair lj/cut/coul/cut mix arithmetic
pair_coeff 6 6 eam Ag_u3.eam

Here is LJ parameter in the data file:

Pair Coeffs

1 lj/cut/coul/cut 0.01084085 4 # S
2 lj/cut/coul/cut 0.003729252 3.816 # C1
3 lj/cut/coul/cut 0.000650451 2.918 # H
4 lj/cut/coul/cut 0.003729252 3.816 # C2
5 lj/cut/coul/cut 0.003729252 3.816 # C3
6 lj/cut/coul/cut 0.001561082 2.805 # Ag

Could some users give me some suggestions? Thank you very much!

2

Dear Lammps Users,

I am simulating the system including metal (Ag) and organic. Interaction
between Ag and organic atoms is LJ potential. For Ag, the potential is EAM.
It includes 6 atom styles and the LJ parameters are in data file. However,
it shows error "All pair coeffs are not set".

this is expected, since your "pair_coeff 6 6..." statement will
overwrite the corresponding entry in the data file and then LAMMPS
cannot determine all mixed terms between atom type 6 and the others.

Here is the input script.

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style charmm

pair_style hybrid lj/cut/coul/cut 10.0 8.0 eam

neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
special_bonds amber

read_data 2016712organic_Ag.data
pair_modify pair lj/cut/coul/cut mix arithmetic
pair_coeff 6 6 eam Ag_u3.eam

Here is LJ parameter in the data file:

Pair Coeffs
1 lj/cut/coul/cut 0.01084085 4 # S
2 lj/cut/coul/cut 0.003729252 3.816 # C1
3 lj/cut/coul/cut 0.000650451 2.918 # H
4 lj/cut/coul/cut 0.003729252 3.816 # C2
5 lj/cut/coul/cut 0.003729252 3.816 # C3
6 lj/cut/coul/cut 0.001561082 2.805 # Ag

Could some users give me some suggestions? Thank you very much!

specify all coefficients, including the mixed terms as pair_coeff statements.

you probably also want to change from lj/cut/coul/cut to
lj/cut/coul/long, or at the very least make your coulomb cutoff
longer, since with 8 angstrom, you will have serious errors due to
truncation of the coulomb potential.

axel.

3

Dear Axel,

Thanks for your reply. How should I modify the input script or data file to exclude the 6 6 type interaction for lj/cut/coul/cut and just consider 6 6 for eam? I try to modify it as below.

Put 1~5 pair coefficients in data file. And 1 6, 2 6, 3 6, 4 6, 5 6, and 6 6 pair coefficients are in input script.

Input script:

pair_style hybrid lj/cut/coul/cut 10.0 8.0 lj/cut/coul/cut 10.0 8.0 lj/cut/coul/cut 10.0 8.0 lj/cut/coul/cut 10.0 8.0 lj/cut/coul/cut 10.0 8.0 lj/cut/coul/cut 10.0 8.0 eam

pair_modify pair lj/cut/coul/cut 1 mix arithmetic

pair_coeff 1 6 lj/cut/coul/cut 2 0.010952671 3.4025
pair_coeff 2 6 lj/cut/coul/cut 3 0.004042809 3.3105
pair_coeff 3 6 lj/cut/coul/cut 4 0.001691173 2.8615
pair_coeff 4 6 lj/cut/coul/cut 5 0.004042809 3.3105
pair_coeff 5 6 lj/cut/coul/cut 6 0.004042809 3.3105
pair_coeff 6 6 eam Ag_u3.eam

Data file:

Pair Coeffs

1 lj/cut/coul/cut 1 0.01084085 4 # S
2 lj/cut/coul/cut 1 0.003729252 3.816 # C1
3 lj/cut/coul/cut 1 0.000650451 2.918 # H
4 lj/cut/coul/cut 1 0.003729252 3.816 # C2
5 lj/cut/coul/cut 1 0.003729252 3.816 # C3

But it shows “ERROR: Unexpected end of PairCoeffs section (…/read_data.cpp:1601)”

4

Dear Axel,

Thanks for your reply. How should I modify the input script or data file to exclude the 6 6 type interaction for lj/cut/coul/cut and just consider 6 6 for eam? I try to modify it as below.

I already made a suggestion.

5

Dear Axel,

Thanks. I know you said that “pair_coeff 6 6…” statement will overwrite the corresponding entry in the data file and then LAMMPS cannot determine all mixed terms between atom type 6 and the others.
I follow your suggestion to try to modify it. But it seems a new error appears. Is my modification incorrect?

6

Dear Axel,

Thanks. I know you said that "pair_coeff 6 6..." statement will overwrite
the corresponding entry in the data file and then LAMMPS cannot determine
all mixed terms between atom type 6 and the others.

you didn't read my entire reply.

I follow your suggestion to try to modify it. But it seems a new error
appears. Is my modification incorrect?

yes. very obviously.