Dear LAMMPS,
I am trying to calculate bond energy (eb) of reax for methane.
My system consists of methane and Ni.
But I would like to avoid Ni part and to analyze eb for methane.
I have tried with compute command, but its not work.
Could you please let me know any possibility how to get eb for methane from my existing system?
This is my script:
group Ni type 1
group C type 2
group H type 3
group bottom type 4
group CH4 type 2 3
####velocity##################
velocity bottom set 0.0 0.0 0.0 units box
Dear LAMMPS,
I am trying to calculate bond energy (eb) of reax for methane.
My system consists of methane and Ni.
But I would like to avoid Ni part and to analyze eb for methane.
I have tried with compute command, but its not work.
it *cannot* work. the compute determines the energy
for an *explicit* bonded interaction, like a harmonic bond
potential. those bonds cannot break and those interactions
don't apply for reax, since there are no explicit bonds.
for what you are looking at, you have to treat a reax
calculation like you would treat a quantum chemical
calculation.
Could you please let me know any possibility how to get eb for methane from
my existing system?
how would you do this with a quantum chemistry code?
If you look at the doc page for the pair_style reax
command, it tells you how to get at lower-level
energy quantities, like eb. If you want eb for
only a portion of the interacting atoms in the system,
I imagine you will need to instrument the code.
The current construction of pair_style reax/c does not allow the
breaking down of lower-level energy components for a subset of atoms.
You might want to follow Axel's advice on how to proceed with this.
I know nothing about the reax potential, and I'm not a quantum
chemist, but I suspect the "rerun" command might be useful in this
kind of situation.
You can run your simulation normally. Then you can compute the energy
of the structures in your trajectory using the "rerun" command. http://lammps.sandia.gov/doc/rerun.html
Before you use "rerun", you can change the input settings so that
atoms which do not belong to methane molecules do not contribute to
the (eb) energy. (I post this reply frequently. "use rerun". I hope
it works in this situation.)