Movaffaq
commented
3 years ago 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
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?