Name: BOPfox file
Extension: .bx
Specification: BOPfox documentation
Visualization programs: none
BOPfox is a program for tight-binding and analytic bond-order potential calculations. When reading files in the BOPfox format, Atomsk will detect if flags are present at the end of each line to define if atoms are fixed along the X, Y, and/or Z direction, and save it as auxiliary properties. If a "magnetisation" section exists, then it will also be stored as auxiliary property. Beware that this information is transferable to some file formats only (see the list of formats).
When writing to the BOPfox format, Atomsk follows the following template:
example.bx
aLat = 1.0
a1 = <H(1,1)> <H(1,2)> <H(1,3)>
a2 = <H(2,1)> <H(2,2)> <H(2,3)>
a3 = <H(3,1)> <H(3,2)> <H(3,3)>
# Natoms = <NP>
coord = Cartesian
<species1> <x1> <y1> <z1> [<F|T> <F|T> <F|T>]
<species2> <x2> <y2> <z2> [<F|T> <F|T> <F|T>]
...
<speciesNP> <xNP> <yNP> <zNP> [<F|T> <F|T> <F|T>]
magnetisation = true
<µx1> <µy1> <µz1>
<µx2> <µy2> <µz2>
...
<µxNP> <µyNP> <µzNP>
The lattice constant (following the keyword aLat) will always be equal to 1. If some atoms are fixed (as defined in the input file or with the option -fix) then the three flags (T or F) will appear at the end of each line, otherwise they are omitted. The section "magnetisation" will be written only if magnetizations (magx, magy, magz) are defined.
atomsk my_system.cfg bx
This will read the file my_system.cfg, and convert it to my_system.bx.
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.bx
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.bx.
atomsk relaxed.bx cfg
This will read the file relaxed.bx, and convert it to relaxed.cfg for visualization with Atomeye or OVITO.