Create bond for ReaxFF
Hello everybody,
i am doing a ReaxFF simulation and here the bonding is implicit and i would like to bond my water molecules ( oxygen to the hydrogens ) and using the pairwise cutoff does not lead to good results since the bonding length changes. My water molecules are ordered this way:
e.g.
1 H (first hydrogen of the 1st molecule )
2 O (oxygen of the first molecule )
3 H (second hydrogen of the 1st molecule )
....
100 H
101 O
102 H
...
How can i bond my oxygens with my hydrogens manually by bonding the oxygen and the two hydrogens with a particle identifier +1 and -1 ?Is it possible with ovito or do i need a full python script for that ?
Best regards
Hi Betim,
the Bond analysis modifier currently only allows to use a distance based criterion, but we are already working on extending its functionality.
In your specific case, you should still be able to solve it with this short python script modifier:
from ovito.data import *
import numpy as np
def modify(frame, data):
bond_topology = []
for i in range(1, 101, 3):
bond_topology.append([i-1, i])
bond_topology.append([i, i+1])
data.particles_.bonds = Bonds()
data.particles_.bonds_.create_property('Topology', data=bond_topology)