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Topology of create bonds
December 17, 2020, 2:27 pm
hello !
I have a problem using the function CreateBondsModifier of ovito.
The topology of bonds is new , it is different from the ParticleIdentifier, and in the track file, the same ID has a different topology.
So, how do I get the ParticleIdentifier through the Topology?
Thank you for your reply in advance.
December 17, 2020, 3:09 pm
Hi,
please note that the topology bond property defines the connectivity between particles in the form of a N x 2 array of indices into the Particles array. As opposed to the particle identifier property, the particle indices are 0-based.
You can use the particle indices from the topology property to look up any corresponding particle property, e.g.
def modify(frame, data):
bond_topology = data.particles.bonds.topology # array with bond topology
# Create bonds enumerator object.
bonds_enum = BondsEnumerator(data.particles.bonds)
# Loop over atoms.
for particle_index in range(data.particles.count):
# Loop over bonds of current atom.
for bond_index in bonds_enum.bonds_of_particle(particle_index):
# Obtain the indices of the two particles connected by the bond:
a,b = bond_topology[bond_index]
print(f"Particle Identifiers:{ data.particles['Particle Identifier'][[a,b]] }")also see https://www.ovito.org/docs/current/scene_objects.bonds.php.