Hello
I want to compute the bond energy of OH molecule in lammps (Morse Potential for Bond), I used compute pe/atom bond and then dumped the energy of each atom but I realized that this energy per atom is due to interaction of each atom with all other atoms in the simulation, not just with other atoms in the group. So, It means the energy that I compute for the OH bond is not the right one…?
( I have Argon atoms in the box with OH, and the Lennard Jones potential for interaction between OH and Ar)
Thank you.
Best,
Leila
Hello
I want to compute the bond energy of OH molecule in lammps (Morse Potential
for Bond), I used compute pe/atom bond and then dumped the energy of each
atom but I realized that this energy per atom is due to interaction of each
atom with all other atoms in the simulation, not just with other atoms in
the group. So, It means the energy that I compute for the OH bond is not the
right one...?
how should anybody know? how can we know that there is no mistake in your input?
if you want clarification, you need to provide an example.
axel.
See the compute bond/local command. It’s output
can be summed by compute reduce or output (bond by bond)
via dump local.
Steve
1 - group Hydroxyl type 2 3
2 - compute 1 Hydroxyl pe/atom bond
3 - compute 2 Hydroxyl ke/atom
4 - dump 1 Hydroxyl custom 20000 dump.pe id c_1 c_2
5 - dump_modify 1 format "%5d %20.10g %20.10g"
6 - dump_modify 1 sort id
and then in the dump file I sum the potential energy of each atom to get the bond energy of OH and kinetic energy of each atom to get the kinetic energy of OH
Best,
Leila
Steve,
It means the way that I did it is wrong.
Thank you for your help.
Best,
Leila