When we want to define covalent bonds across periodic simulation box (in case if we want to simulate the behavior of complex crystals like tobermorite), can we use create bonds command.
My specific question is if we specify " rmin = minimum distance between pair of atoms to bond together
and rmax = maximum distance between pair of atoms to bond together " and also atom types that need to be bonded together across boundary, accurately in create bond command, will covalent bonds get created across boundaries or it can be only used for defining bonds inside simulation box.
I understood that, practically I cannot go with this method where we want to define bonds across simulation box individually.
Since i am working with tobermorite supercell, where a large number of bonds across boundaries have to be defined, can you suggest some relatively easier approach for this purpose.
My concern would be less about the bonds, but that typical molecular force fields may require creating more topological information than just bonds, but angles and potentially dihedrals as well. Assuming that create_bonds can create bonds across periodic boundaries (it uses the neighborlist in which the prerequiste pairs of atoms are present, if the neighbor list and communication cutoff are sufficiently large), how would you then derive other interactions based on those bonds?
For the benefit of people that find this discussion when looking for advice on similar problems, here is a simple input to demonstrate how one can create an input verifying some functionality with just a minimal effort. This will create just 3 atoms in a box and then creates bonds between them. Data files and images are created for confirmation.
atom_style bond
region box block 0 3 0 3 0 3
create_box 1 box bond/types 1 extra/bond/per/atom 4 extra/special/per/atom 4
create_atoms 1 single 0.5 0.5 1.5
create_atoms 1 single 0.5 1.5 1.5
create_atoms 1 single 0.5 2.5 1.5
mass 1 1.0
pair_style zero 5.0
pair_coeff 1 1
bond_style zero
bond_coeff 1 1.0
write_data nobonds.data
write_dump all image nobonds.png type type modify adiam 1 0.8
create_bonds many all all 1 0.1 1.1
write_data cyclical.data
write_dump all image cyclical.png type type modify adiam 1 0.8
To check whether this works in multiple dimensions one can add the following commands:
create_atoms 1 single 1.5 0.5 1.5
create_atoms 1 single 1.5 1.5 1.5
create_atoms 1 single 1.5 2.5 1.5
create_atoms 1 single 2.5 0.5 1.5
create_atoms 1 single 2.5 1.5 1.5
create_atoms 1 single 2.5 2.5 1.5
write_dump all image partbonds.png type type modify adiam 1 0.8
create_bonds many all all 1 0.1 1.1
write_data sheet.data
write_dump all image sheet.png type type modify adiam 1 0.8
