OVITO create bonds crossing periodic boundary conditions using python

OVITO
1

Dear OVITO users and developers,

I am using ovito to create bonds across pbc, and then export LAMMPS DATA file.
In GUI, it is easy to be done by enabling x, y, z pbc under Simulation Cell. However, I have a lot of systems to build so it would be super tedious to click click click.
So I am trying to write a python script to do that, but I met a problem in enabling pbc in python. Here is my code:

pipeline = import_file(trjs)
create_bonds_modifier = CreateBondsModifier(mode=CreateBondsModifier.Mode.Pairwise)
create_bonds_modifier.set_pairwise_cutoff(type_a=6,type_b=7,cutoff=1.01)
pipeline.modifiers.append(create_bonds_modifier)
data = pipeline.compute()

print(data.cell_.pbc) # output: False, False, False
print(data.particles.bonds.count) # output: wrong bond number

I noticed that ovito manual mentions this pbc problem, bond vectors?

image
image836×491 51.1 KB

but it does not mention how to use this bond vectors to create bonds.
Anyone can help me? Thanks!

Bests,
Jay

2 
def set_pbc(frame,data):
    data.cell_.pbc = (True,True,True)

def create_bonds_ovito():
    pipeline = import_file(trjs)
    pipeline.modifiers.append(set_pbc)
    create_bonds_modifier = CreateBondsModifier(mode=CreateBondsModifier.Mode.Pairwise)
    create_bonds_modifier.set_pairwise_cutoff(type_a=6,type_b=7,cutoff=1.01)
    pipeline.modifiers.append(create_bonds_modifier)
    data = pipeline.compute()
    
    print(data.cell_.pbc) # output: True, True, True
    print(data.particles.bonds.count) # output: correct bond number

    export_file(data,'filename.data','lammps/data',atom_style='full')
3

I made some minor formatting changes to your code so that it can be used for future reference. I assume you successfully solved your problem?

4

Yes, it worked！ Thanks！

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