Thanks a lot for your answer really, Steve.
I’ve made data file (data.graphene) for graphene using topotools of VMD from pdb file following advice of Axel (many thanks for it, Axel).
I think I should edit it afterward to meet my system.
I’d like to use airebo potential and I’ve read “read data” parts of manual carefully.
However, I have six questions on it as follows and anaswers on them would help me to understand LAMMPS greatly.
- I suppose molecule ID is not required additionally for my system and the format of “atom_ID atom_type coord_x coord_y coord_z” will be sufficient for “Atoms section”.
In addition, here, atom_type should be 1 if I write “pair_coeff * * CH.airebo C” in my input file.
That is, the following may be O.K.
1 1 17.028999 34.431000 5.132000 # C1 1
2 1 17.028999 7.371000 5.132000 # C2 1
What do you think on it?
The format for Bonds section is “bond_ID bond_type ID_1st_atom ID_2nd_atom”.
Here, where is bond_type defined generally?
If I use airebo potential, is it described in CH.airebo? (It is hard to find bond_type notation in that file.)
What should I write bond_type for graphene using airebo potential?
Should bond_type be “1”?
There are only atoms and bonds section in data.graphene made from topotools.
If I use airebo potential for graphene (which is composed of carbon only and, maybe, there will be merely one atom type carbon, I guess.), will other sections for angle, dihedral,improper etc. be needless?
In questions 3, if sections for angle, dihedral, improper are also required in the use of airebo potential, where can I find description for types (1~ Ntypes for angle_type, dihedral_type, improper type) of angle, dihedral, improper?
I use periodic boundary condition for my system.
In spite of the use of PBC, may I omit optional arguements of nx,ny,nz (for image)?
That is, will LAMMPS consider the most closed atom for a certain atom_ID automatically (considering various image ones)?
Generally speaking (not only for CH.airebo), where can I find detailed “type description” for each sections (Bonds, Angles, etc.)?