Dear all,
I am using “reax/c/species” to see what product has formed.
But, the result is different with “xyz trajectory”.
result from reax/c/species says the molecule has been broken, but when I check the structure with jmol or material studio(visualization tool) there is no bond breaking…
I modified “bond_graph_cutoff” parameter to 0.2 or 0.4. But, it didn’t work.
more detail, reax/c/species says there is single H, but all hydrogen is bonded with some other atoms.
Thanks
Dear all,
I am using “reax/c/species” to see what product has formed.
please always report the version of LAMMPS that you are using.
But, the result is different with “xyz trajectory”.
result from reax/c/species says the molecule has been broken, but when I check the structure with jmol or material studio(visualization tool) there is no bond breaking…
fix reax/c/species uses the bond-order parameter computed by pair style reax/c to determine whether bonds are formed or not.
that should be much more reliable than any heuristics employed by visualization tools. some visualization tools won’t even re-evaluate bond topology for each shown time step. i don’t use the two tools you mention, so i cannot comment on their abilities and limitations specifically.
I modified “bond_graph_cutoff” parameter to 0.2 or 0.4. But, it didn’t work.
more detail, reax/c/species says there is single H, but all hydrogen is bonded with some other atoms.
please provide a simple, small, and concise test case reproducing what you think is incorrect behavior and make certain it can reproduce this behavior with the latest LAMMPS patch version.
axel.