Name: Bond-Order Potential file
Extension: unspecified (Atomsk uses .bop)
Specification: N/A
Visualization programs: none
When reading files in the BOP format, Atomsk will store the state of each atom (free or fixed) as auxiliary properties (fixed atoms will be fixed along the X, Y and Z axes). Beware that this information is transferable to some file formats only (see the list of formats).
When writing to the BOP format Atomsk will use the following format:
example.bop
A
<H(1,1)> <H(1,2)> <H(1,3)>
<H(2,1)> <H(2,2)> <H(2,3)>
<H(3,1)> <H(3,2)> <H(3,3)>
LEN
1.0 1.0 1.0
LATPAR
1.000
ND
<Nfree>
D
<x1> <y1> <z1> <species1> 0.000
<x2> <y2> <z2> <species2> 0.000
...
<xND> <yND> <zND> <speciesND> 0.000
NINERT
<Nfixed>
DINERT
<x1> <y1> <z1> <species1> 0.000
<x2> <y2> <z2> <species2> 0.000
...
<xNINERT> <yNINERT> <zNINERT> <speciesNINERT> 0.000
The scaling vectors (following the keyword LEN) will all be equal to 1, as is the lattice parameter (following LATPAR). Atoms that are fixed (as defined in the input file or with the option -fix) in one or more directions will appear in the DINERT section.
atomsk my_system.cfg bop
This will read the file my_system.cfg, and convert it to my_system.bop.
atomsk unitcell.xsf -duplicate 20 20 1 -disloc 0.5*BOX 0.5*BOX screw z y 4.2 0.33 -select out box 10 10 -INF BOX-10 BOX-10 INF -fix all above -100 x my_system.bop
This will read the file unitcell.xsf, duplicate it to form a 20x20x1 supercell, then insert a screw dislocation in the middle of the box and along the Z direction, select atoms that are within 10 Å to the box edges, fix these atoms, and write the final configuration to my_system.bop.
atomsk relaxed.bop cfg
This will read the file relaxed.bop, and convert it to relaxed.cfg for visualization with Atomeye.