Hello,
I am trying to figure out an efficient way of exporting the bond
information (or neighbor list). The reax/c package and LAMMPS CHO
example is used as the initial example.
In LAMMPS' tools folder, there is "reax_bond.pl" which seems to be
written for this purpose. I tried it, but it gives me a large number
of empty temp files and a list of frames in a "frac.dat". Is there any
manual on this file by any chance?
As another try I compiled a MATLAB script to read the atoms
information from dump files for each frame, and consider each 2 atom
with their distance smaller than a certain cut-off length (1.9),
covalent bonded. It is based on a "coordinate number" concept. Does it
sound correct?
I am assuming the "fix reax/c/bonds" command does not help much during
the simulation, as it invokes "pair_style reax/c". It should be only
helpful if it is used at the very end of the simulation. Am I correct?
Many thanks for your help,
Ardavan
Comments below, thanks.
Ray
In LAMMPS' tools folder, there is "reax_bond.pl" which seems to be
written for this purpose. I tried it, but it gives me a large number
of empty temp files and a list of frames in a "frac.dat". Is there any
manual on this file by any chance?
You will have to ask the original author of the tool for a manual or
instructions.
Please see "fix reax/c/bonds" doc page, which does what you are trying
to do. "mol_fra.c" in tools/reax analyzes the output of this fix.
As another try I compiled a MATLAB script to read the atoms
information from dump files for each frame, and consider each 2 atom
with their distance smaller than a certain cut-off length (1.9),
covalent bonded. It is based on a "coordinate number" concept. Does it
sound correct?
Seems this can be done with "compute cluster/atom", which is based on
bond distance-cutoff, while "fix reax/c/bond" is based on bond
order-cutoff.
I am assuming the "fix reax/c/bonds" command does not help much during
the simulation, as it invokes "pair_style reax/c". It should be only
helpful if it is used at the very end of the simulation. Am I correct?
No. Please read the "fix reax/c/bonds" doc page.
Ray,
Thanks. It sounds reasonable and helpful.
Ardavan