Lammps simulation

[xk-liu]

Thanks for providing the tool to build the graphene-oxide structure. When I use the produced data file for lammps, I find the file appears to have some redundancy. For instance, the following contents can be found in the file GO_stack.data
Masses
1 12.011
2 1.008
3 12.011
4 15.999
5 1.008
6 15.999
7 15.999
8 12.011
9 15.999
10 15.999
11 12.011
12 12.011
13 15.999
354 40.08
349 22.99
Pair Coeffs
1 0.07 3.55
2 0.03 2.42
3 0.066 3.5
4 0.17 3.12
5 0.0 0.0
6 0.14 2.9
7 0.17 3.07
8 0.105 3.75
9 0.21 2.96
10 0.17 3.0
11 0.07 3.55
12 0.105 3.75
13 0.21 2.96
354 0.449657 2.412031
349 0.0005 4.07

However, there are no atoms with type 12, 13, 354, 349. So I delete the related lines and modify the number of ”atom types ”and ”bond types”. However, when the modified file is used in a lammps simulation, the system just crashes after a minimization process. I am not sure if this is caused by the force field parameters. Could you please provide some clues?

[Movaffaq]

Thanks for providing the tool to build the graphene-oxide structure. When I use the produced data file for lammps, I find the file appears to have some redundancy. For instance, the following contents can be found in the file GO_stack.data
Masses
1 12.011
2 1.008
3 12.011
4 15.999
5 1.008
6 15.999
7 15.999
8 12.011
9 15.999
10 15.999
11 12.011
12 12.011
13 15.999
354 40.08
349 22.99
Pair Coeffs
1 0.07 3.55
2 0.03 2.42
3 0.066 3.5
4 0.17 3.12
5 0.0 0.0
6 0.14 2.9
7 0.17 3.07
8 0.105 3.75
9 0.21 2.96
10 0.17 3.0
11 0.07 3.55
12 0.105 3.75
13 0.21 2.96
354 0.449657 2.412031
349 0.0005 4.07

However, there are no atoms with type 12, 13, 354, 349. So I delete the related lines and modify the number of ”atom types ”and ”bond types”. However, when the modified file is used in a lammps simulation, the system just crashes after a minimization process. I am not sure if this is caused by the force field parameters. Could you please provide some clues?

xk-liu,
You can fix this manually by correcting atom types (max 13), masses (remove 349 and 354) and pair coeffs (remove 349 349 and 354 354). Whitin your python script I suggest the following if you don't need carboxylate groups and thus cations:

vdw_defs = {
1: 90, # Cg, graphitic (aromatic)
2: 91, # Hg, graphitic edge
3: 101, # Ct, tertiary C-OH
4: 96, # Oa, C-OH
5: 97, # Ha, C-OH
6: 122, # Oe, epoxy
7: 109, # Oa, C-OH
8: 209, # Cc, Carboxylic carbon
9: 210, # Oc, Ketone oxygen
10: 211, # Oa, alcohol
11: 108, # Cb, Benzyl
}
mg.Parameterise(flake, vdw_defs)
you should also change the flake with your oxidiser output.
Regards,
Movaffaq Kateb